Fusion proteins of mycobacterium tuberculosis

ABSTRACT

The present invention relates to compositions and fusion proteins containing at least two Mycobacterium sp. antigens, and nucleic acids encoding such compositions and fusion proteins. The compositions of the invention increase serological sensitivity of sera from individuals infected with tuberculosis, and methods for their use in the diagnosis, treatment, and prevention of tuberculosis infection.

CROSS-REFERENCES TO RELATED APPLICATIONS

[0001] The present application claims priority to U.S. patent application Ser. No. 09/597,796, filed Jun. 20, 2000, and U.S. patent application Ser. No. 60/265,737, filed Feb. 1, 2001, herein each incorporated by reference in their entirety.

[0002] The present application is related to U.S. patent application Ser. No. 09/056,556, filed Apr. 7, 1998; U.S. patent application Ser. No. 09/223,040, filed Dec. 30, 1998; U.S. patent application Ser. No. 09/287,849, filed Apr. 7, 1999; published PCT application No. WO99/51748, filed Apr. 7, 1999 (PCT/US99/07717), U.S. patent application Ser. No. 60/158,338, filed Oct. 7, 1999, and U.S. application Ser. No. 60/158,425, filed Oct. 7, 1999; U.S. application Ser. No. 09/688,672, filed Oct. 10, 2000; and published PCT application No. WO01/24820, filed Oct. 10, 2000 (PCT/US00/28095); herein each incorporated by reference in its entirety.

STATEMENT AS TO RIGHTS TO INVENTIONS MADE UNDER FEDERALLY SPONSORED RESEARCH AND DEVELOPMENT

[0003] Not applicable.

FIELD OF THE INVENTION

[0004] The present invention relates to fusion proteins containing at least two Mycobacterium sp. antigens. In particular, it relates to nucleic acids encoding fusion proteins that include two or more individual M. tuberculosis antigens, which increase serological sensitivity of sera from individuals infected with tuberculosis, and methods for their use in the diagnosis, treatment, and prevention of tuberculosis infection.

BACKGROUND OF THE INVENTION

[0005] Tuberculosis is a chronic infectious disease caused by infection with M. tuberculosis and other Mycobacterium species. It is a major disease in developing countries, as well as an increasing problem in developed areas of the world, with about 8 million new cases and 3 million deaths each year. Although the infection may be asymptomatic for a considerable period of time, the disease is most commonly manifested as an acute inflammation of the lungs, resulting in fever and a nonproductive cough. If untreated, serious complications and death typically result.

[0006] Although tuberculosis can generally be controlled using extended antibiotic therapy, such treatment is not sufficient to prevent the spread of the disease. Infected individuals may be asymptomatic, but contagious, for some time. In addition, although compliance with the treatment regimen is critical, patient behavior is difficult to monitor. Some patients do not complete the course of treatment, which can lead to ineffective treatment and the development of drug resistance.

[0007] In order to control the spread of tuberculosis, effective vaccination and accurate early diagnosis of the disease are of utmost importance. Currently, vaccination with live bacteria is the most efficient method for inducing protective immunity. The most common mycobacterium employed for this purpose is Bacillus Calmette-Guerin (BCG), an avirulent strain of M. bovis. However, the safety and efficacy of BCG is a source of controversy and some countries, such as the United States, do not vaccinate the general public with this agent.

[0008] Diagnosis of tuberculosis is commonly achieved using a skin test, which involves intradermal exposure to tuberculin PPD (protein-purified derivative). Antigen-specific T cell responses result in measurable induration at the injection site by 48-72 hours after injection, which indicates exposure to mycobacterial antigens. Sensitivity and specificity have, however, been a problem with this test, and individuals vaccinated with BCG cannot be distinguished from infected individuals.

[0009] While macrophages have been shown to act as the principal effectors of Mycobacterium immunity, T cells are the predominant inducers of such immunity. The essential role of T cells in protection against Mycobacterium infection is illustrated by the frequent occurrence of Mycobacterium infection in AIDS patients, due to the depletion of CD4⁺ T cells associated with human immunodeficiency virus (HIV) infection. Mycobacterium-reactive CD4⁺ T cells have been shown to be potent producers of γ-interferon (IFN-γ), which, in turn, has been shown to trigger the anti-mycobacterial effects of macrophages in mice. While the role of IFN-γ in humans is less clear, studies have shown that 1,25-dihydroxy-vitamin D3, either alone or in combination with IFN-γ or tumor necrosis factor-alpha, activates human macrophages to inhibit M. tuberculosis infection. Furthermore, it is known that IFN-γ stimulates human macrophages to make 1,25-dihydroxy-vitamin D3. Similarly, interleukin-12 (IL-12) has been shown to play a role in stimulating resistance to M. tuberculosis infection. For a review of the immunology of M tuberculosis infection, see Chan & Kaufmann, Tuberculosis: Pathogenesis, Protection and Control (Bloom ed., 1994), and Harrison 's Principles of Internal Medicine, volume 1, pp. 1004-1014 and 1019-1023 (14^(th) ed., Fauci et al., eds., 1998).

[0010] Accordingly, there is a need for improved diagnostic reagents, and improved methods for diagnosis, preventing and treating tuberculosis.

SUMMARY OF THE INVENTION

[0011] The present invention therefore provides compositions comprising at least two heterologous antigens, fusion proteins comprising the antigens, and nucleic acids encoding the antigens, where the antigens are from a Mycobacterium species from the tuberculosis complex and other Mycobacterium species that cause opportunistic infections in immune compromised patients. The present invention also relates methods of using the polypeptides and polynucleotides in the diagnosis, treatment and prevention of Mycobacterium infection.

[0012] In one aspect, the present invention provides compositions and fusion proteins comprising a mutated version of Ra35 (N-terminal portion of MTB32A) or Ra35FL (full length MTB32A), in which one, two, or three of the three amino acids histidine, aspartate, or serine at the active site has been mutated to a different amino acid. In one embodiment, in Ra35FL, the serine at position 183 has been mutated to an alanine residue, creating Ra35FLMutSA. In one embodiment, the DNA encoding Ra35FL has been mutated by changing a T to a G, resulting in a serine to alanine mutation at amino acid 183 of SEQ ID NO:4. In another embodiment, the present invention provides the fusion protein MTB72FMutSA, in which the Ra35 component of the fusion protein has a serine to alanine mutation at amino acid position 710 of the MTB72F sequence. In another embodiment, the present invention provides a nucleic acid encoding the fusion protein MTB72F, in which the nucleic acid encoding the Ra35 component has been mutated by changing a T to a G, resulting in a serine to alanine mutation at amino acid position 710 of the MTB72F sequence.

[0013] The present invention is based, in part, on the inventors' discovery that fusion polynucleotides, fusion polypeptides, or compositions that contain at least two heterologous M. tuberculosis coding sequences or antigens are highly antigenic and upon administration to a patient increase the sensitivity of tuberculosis sera. In addition, the compositions, fusion polypeptides and polynucleotides are useful as diagnostic tools in patients that may have been infected with Mycobacterium.

[0014] In one aspect, the compositions, fusion polypeptides, and nucleic acids of the invention are used in in vitro and in vivo assays for detecting humoral antibodies or cell-mediated immunity against M tuberculosis for diagnosis of infection or monitoring of disease progression. For example, the polypeptides may be used as an in vivo diagnostic agent in the form of an intradermal skin test. The polypeptides may also be used in in vitro tests such as an ELISA with patient serum. Alternatively, the nucleic acids, the compositions, and the fusion polypeptides may be used to raise anti-M. tuberculosis antibodies in a non-human animal. The antibodies can be used to detect the target antigens in vivo and in vitro.

[0015] In another aspect, the compositions, fusion polypeptides and nucleic acids may be used as immunogens to generate or elicit a protective immune response in a patient. The isolated or purified polynucleotides are used to produce recombinant fusion polypeptide antigens in vitro, which are then administered as a vaccine. Alternatively, the polynucleotides may be administered directly into a subject as DNA vaccines to cause antigen expression in the subject, and the subsequent induction of an anti-M. tuberculosis immune response. Thus, the isolated or purified M. tuberculosis polypeptides and nucleic acids of the invention may be formulated as pharmaceutical compositions for administration into a subject in the prevention and/or treatment of M. tuberculosis infection. The immunogenicity of the fusion protein or antigens may be enhanced by the inclusion of an adjuvant, as well as additional fusion polypeptides, from Mycobacterium or other organisms, such as bacterial, viral, mammalian polypeptides. Additional polypeptides may also be included in the compositions, either linked or unlinked to the fusion polypeptide or compositions.

BRIEF DESCRIPTION OF THE DRAWINGS

[0016]FIG. 1 shows percent survival of Guinea pigs vaccinated with MTB72F polyprotein.

[0017]FIG. 2 shows CFUs from spleen cells (FIG. 2A) and lung cells after immunization with MTB72F, MTB59F, MTB72F DNA, or a composition comprising Ra12, TbH9, and Ra35 antigens.

[0018]FIG. 3 shows a schematic diagram of MTB72F.

[0019]FIG. 4 shows the nucleotide and amino acid sequence of Ra35 (195 amino acids from the N-terminal portion of MTB32A).

[0020]FIG. 5 shows an alignment of the amino acid sequences of MTB72F and the mutated version MTB72FMutSA.

[0021]FIG. 6 shows an alignment of the amino acid sequences of mature (full length) Ra35/MTB32A and the mutated version Ra35FLMutSA.

[0022]FIG. 7 shows long term survival of guinea pigs vaccinated with Mtb72F formulations.

DESCRIPTION OF THE SPECIFIC EMBODIMENTS

[0023] The present invention relates to compositions comprising antigen compositions and fusion polypeptides useful for the diagnosis and treatment of Mycobacterium infection, polynucleotides encoding such antigens, and methods for their use. The antigens of the present invention are polypeptides or fusion polypeptides of Mycobacterium antigens and immunogenic thereof. More specifically, the compositions of the present invention comprise at least two heterologous polypeptides of a Mycobacterium species of the tuberculosis complex, e.g., a species such as M tuberculosis, M. bovis, or M africanum, or a Mycobacterium species that is environmental or opportunistic and that causes opportunistic infections such as lung infections in immune compromised hosts (e.g., patients with AIDS), e.g., BCG, M avium, M. intracellulare, M. celatum, M. genavense, M haemophilum, M kansasii, M simiae, M. vaccae, M. fortuitum, and M scrofulaceum (see, e.g., Harrison 's Principles of Internal Medicine, volume 1, pp. 1004-1014 and 1019-1023 (14^(th) ed., Fauci et al., eds., 1998). The inventors of the present application surprisingly discovered that compositions and fusion proteins comprising at least two heterologous Mycobacterium antigens, or immunogenic fragments thereof, where highly antigenic. These compositions, fusion polypeptides, and the nucleic acids that encode them are therefore useful for eliciting protective response in patients, and for diagnostic applications.

[0024] The antigens of the present invention may further comprise other components designed to enhance the antigenicity of the antigens or to improve these antigens in other aspects, for example, the isolation of these antigens through addition of a stretch of histidine residues at one end of the antigen. The compositions, fusion polypeptides, and nucleic acids of the invention can comprise additional copies of antigens, or additional heterologous polypeptides from Mycobacterium sp., such as MTB8.4 antigen, MTB9.8 antigen, MTB9.9 antigen, MTB40 antigen, MTB41 antigen, 38-1, TbRa3, 38 kD, DPEP, TbH4, DPPD, ESAT-6 antigen, MTB85 complex antigen (e.g., MTB85b), or α-crystalline antigen, and Erd14. The compositions, fusion polypeptides, and nucleic acids of the invention can also comprise additional heterologous polypeptides from other non-Mycobacterium sources. For example, the compositions and fusion proteins of the invention can include polypeptides or nucleic acids encoding polypeptides, wherein the polypeptide enhances expression of the antigen, e.g., NS1, an influenza virus protein, or an immunogenic portion thereof (see, e.g. WO99/40188 and WO93/04175). The nucleic acids of the invention can be engineered based on codon preference in a species of choice, e.g., humans.

[0025] The compositions of the invention can be naked DNA, or the compositions, e.g., polypeptides can also comprise adjuvants, e.g., MPL, 3D-MPL, IFA, AS adjuvants such as AS2, AS2′, AS2″, AS4, AS6, ENHANZYN (Detox), QS21, CWS, TDM, AGP, CPG, Leif, saponin, and saponin mimetics, and derivatives thereof. In addition, the compositions of the invention can comprise BCG or Pvac as an adjuvant.

[0026] In one embodiment, the compositions and fusion proteins of the invention are composed of at least two antigens selected from the group consisting of a MTB39 antigen or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a MTB32A antigen or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex.

[0027] In another embodiment, the antigens are selected from the group consisting of a MTB39 antigen or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a polypeptide comprising at least 205 amino acids of the N-terminus of a MTB32A antigen from a Mycobacterium species of the tuberculosis complex.

[0028] In another embodiment, the antigens are selected from the group consisting of a MTB39 antigen or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, a polypeptide comprising at least about 205 amino acids of the N-terminus of a MTB32A antigen from a Mycobacterium species of the tuberculosis complex, and a polypeptide comprising at least about 132 amino acids from the C-terminus of MTB32A antigen from a Mycobacterium species of the tuberculosis complex.

[0029] In the nomenclature of the application, Ra35 refers to the N-terminus of MTB32A (Ra35FL), comprising at least about 195 to 205 amino acids of MTB32A from M. tuberculosis, or the corresponding region from another Mycobacterium species. Ra12 refers to the C-terminus of MTB32A (Ra35FL), comprising at least about the last 132 amino acids from MTB32A from M. tuberculosis, or the corresponding region from another Mycobacterium species.

[0030] The following provides sequences of some antigens used in the compositions and fusion proteins of the invention:

[0031] SEQ ID NO:1-4: MTB32A (Ra35FL or Ra35 mature), the sequence of which is also disclosed as SEQ ID NO:17 (cDNA) and SEQ ID NO:79 (protein) in the U.S. patent applications Ser. No. 08/523,436, 08/523,435, No. 08/658,800, No. 08/659,683, No. 08/818,112, No. 09/056,556, and No. 08/818,111 and in the WO97/09428 and WO97/09429 applications, see also Skeiky et al., Infection and Immunity 67:3998-4007 (1999). The term MTB32A also includes MTB32A amino acid sequences in which any one of the three amino acids at the active site triad (His, Asp, Ser), e.g., the serine residue at amino acid position 207 in SEQ ID NO:2 or amino acid position 183 in SEQ ID NO:4, has been changed to another amino acid (e.g., alanine, Ra35FLMutSA, see, e.g., FIG. 6 and SEQ ID NO:6).

[0032] SEQ ID NO:5 and 6: Ra35FLMut SA, the mature version of RA35FL in which the serine residue at amino acid position 183 of SEQ ID NO:4 has been changed to an alanine residue.

[0033] SEQ ID NO:7 and 8: Ra35, the N-terminus of MTB32A (Ra35FL), comprising at least about 195 amino acids from the N-terminus of MTB32A from M. tuberculosis, the nucleotide and amino acid sequence of which is disclosed in FIG. 4 (see also amino acids 33-227 of SEQ ID NO:2 and amino acids 8 to 202 of SEQ ID NO:4). The term Ra35 (N-term) also includes Ra35 amino acid sequences in which any one of the three amino acids at the active site triad (i.e., His, Asp, or Ser) has been changed as described above.

[0034] SEQ ID NO:9 and 10: MTBRa12, the C-terminus of MTB32A (Ra35FL), comprising at least about 132 amino acids from the C-terminus of MTB32A from M. tuberculosis (see, e.g., amino acids 224 to 355 of SEQ ID NO:2 and amino acids 199 to 330 of SEQ ID NO:4), the sequence of which is disclosed as SEQ ID NO:4 (DNA) and SEQ ID NO:66 (predicted amino acid sequence) in the U.S. patent application Ser. No. 09/072,967.

[0035] SEQ ID NO:11, 12, 13, and 14: MTB39 (TbH9), the sequence of which is disclosed as SEQ ID NO:106 (cDNA full length) and SEQ ID NO:107 (protein full length) in the U.S. patent applications Ser. No. 08/658,800, No. 08/659,683, No. 08/818,112, and No. 08/818,111 and in the WO97/09428 and WO97/09429 applications. The sequence is also disclosed as SEQ ID NO:33 (DNA) and SEQ ID NO:91 (amino acid) in U.S. patent application Ser. No. 09/056,559.

[0036] The following provides sequences of some fusion proteins of the invention

[0037] SEQ ID NO:15 and 16: MTB72F (Ra12-TbH9-Ra35), the sequence of which is disclosed as SEQ ID NO:1 (DNA) and SEQ ID NO:2 (protein) in the U.S. patent application Ser. No. 09/223,040, No. 09/223,040, and in the PCT/US99/07717 application. The term MTB372F also includes MTB72F amino acid sequences in which any one of the three amino acids at the active site triad in Ra35FL (i.e., His, Asp, or Ser), has been changed as described above (see, e.g., MTB72FMutSA, FIG. 5).

[0038] SEQ ID NO:17 and 18: MTB72FMutSA (Ra12-TbH9-Ra35MutSA), wherein, in the Ra35 component of the fusion protein, the serine at position 710 has been changed to an alanine.

[0039] SEQ ID NO:19 and 20: TbH9-Ra35 (MTB59F), the sequence of which is disclosed as SEQ ID NO:23 (cDNA) and SEQ ID NO:24 (protein) in the U.S. patent application Ser. No. 09/287,849 and in the PCT/US99/07717 application.

[0040] The following provides sequences of some additional antigens used in the compositions and fusion proteins of the invention:

[0041] SEQ ID NO: 21 and 22: MTB8.4 (DPV), the sequence of which is disclosed as SEQ ID NO:101 (cDNA) and SEQ ID NO:102 (protein) in the U.S. patent applications Ser. No. 08/658,800, No. 08/659,683, No. 08/818,112 and No. 08/818,111 and in the WO97/09428 and WO97/09429 applications.

[0042] SEQ ID NO:23 and 24: MTB9.8 (MSL), the sequence of which is disclosed as SEQ ID NO:12 (DNA), SEQ ID NO:109 (predicted amino acid sequence) and SEQ ID NO:110 to 124 (peptides) in the U.S. patent applications Ser. No. 08/859,381, No. 08/858,998, No. 09/073,009 and No. 09/073,010 and in the PCT/US98/10407 and PCT/US98/10514 applications.

[0043] SEQ ID NO:25, 26, and 27: MTB9.9A (MTI, also known as MTI-A), the sequence of which is disclosed as SEQ ID NO:3 and SEQ ID NO:4 (DNA) and SEQ ID NO:29 and SEQ ID NO:51 to 66 (ORF peptide for MTI) in the U.S. patent applications Ser. No. 08/859,381, No. 08/858,998, No. 09/073,009 and v09/073,010 and in the PCT/US98/10407 and PCT/US98/10514 applications. Two other MTI variants also exist, called MTI-B and MTI-C.

[0044] SEQ ID NO:28 and 29: MTB40 (HTCC#1), the sequence of which is disclosed as SEQ ID NO:137 (cDNA) and 138 (predicted amino acid sequence) in the U.S. patent applications Ser. No. 09/073,009 and No. 09/073,010 and in the PCT/US98/10407 and PCT/US98/10514 applications.

[0045] SEQ ID NO:30 and 31: MTB41 (MTCC#2), the sequence of which is disclosed as SEQ ID NO:140 (cDNA) and SEQ ID NO:142 (predicted amino acid sequence) in the U.S. patent applications Ser. No. 09/073,009 and No. 09/073,010 and in the PCT/US98/10407 and PCT/US98/10514 applications.

[0046] SEQ ID NO:32 and 33: ESAT-6, the sequence of which is disclosed as SEQ ID NO:103 (DNA) and SEQ ID NO:104 (predicted amino acid sequence) in the U.S. patent application Ser. No. 09/072,967. The sequence of ESAT-6 is also disclosed in U.S. Pat. No. 5,955,077.

[0047] SEQ ID NO:34 and 35: Tb38-1 or 38-1 (MTb11), the sequence of which is disclosed in SEQ ID NO:46 (DNA) and SEQ ID NO:88 (predicted amino acid) in the U.S. patent application Ser. Nos. 09/072,96; 08/523,436; 08/523,435; 08/818,112; and 08/818,111; and in the WO97/09428 and WO97/09429 applications.

[0048] SEQ ID NO:36 and 37: TbRa3, the sequence of which is disclosed in SEQ ID NO:15 (DNA) and SEQ ID NO:77 (predicted amino acid sequence) of WO 97/09428 and WO97/09429 applications.

[0049] SEQ ID NO:38 and 39: 38 kD, the sequence of which is disclosed in SEQ ID NO:154 (DNA) and SEQ ID NO:155 (predicted amino acid sequence) in the U.S. patent application Ser. No. 09/072,967. 38 kD has two alternative forms, with and without the N-terminal cysteine residue.

[0050] SEQ ID NO:40 and 41: DPEP, the sequence of which is disclosed in SEQ ID NO:52 (DNA) and SEQ ID NO:53 (predicted amino acid sequence) in the WO97/09428 and WO97/09429 publications.

[0051] SEQ ID NO:42 and 43: TbH4, the sequence of which is disclosed as SEQ ID NO:43 (DNA) and SEQ ID NO:81 (predicted amino acid sequence) in WO97/09428 and WO97/09429 publications.

[0052] SEQ ID NO:44 and 45: DPPD, the sequence of which is disclosed in SEQ ID NO:240 (DNA) and SEQ ID NO:241 (predicted amino acid sequence) in U.S. Ser. No. 09/072,967 and in the PCT/US99/03268 and PCT/US99/03265 applications. The secreted form of DPPD is shown herein in FIG. 12 of PCT/US00/28095.

[0053] MTb82 (MTb867), the sequence of which is disclosed in FIGS. 8 (DNA) and 9 (amino acid) of PCT/US00/2809.

[0054] Erd14 (MTb16), the cDNA and amino acids sequences of which are disclosed in Verbon et al., J. Bacteriology 174:1352-1359 (1992).

[0055] α-crystalline antigen, the sequence of which is disclosed in Verbon et al., J. Bact. 174:1352-1359 (1992);

[0056] 85 complex antigen, e.g., 85b antigen, the sequence of which is disclosed in Content et al., Infect. & Immunol. 59:3205-3212 (1991).

[0057] The following provides sequences of some additional fusion proteins used in the compositions and fusion proteins of the invention:

[0058] SEQ ID NO:46 and 47: DPV-MTI-MSL-MTCC#2 (MTb71F), the sequence of which is disclosed as SEQ ID NO:15 (nucleic acid) and in SEQ ID NO:16: (protein) in the U.S. patent application Ser. No. 09/287,849 and in the PCT/US99/07717 application.

[0059] SEQ ID NO:48 and 49: DPV-MTI-MSL (MTb31F), the sequence of which is disclosed in SEQ ID NO:18 (cDNA) and SEQ ID NO:19 (protein) in the U.S. patent application Ser. No. 09/287,849 and in the PCT/US99/07717 application.

[0060] Each of the above sequences is also disclosed in Cole et al. Nature 393:537 (1998) and can be found at, e.g., http://www.sanger.ac.uk and http:/www.pasteur.fr/mycdb/.

[0061] The above sequences are disclosed in U.S. patent applications Ser. Nos. 08/523,435, 08/523,436, 08/658,800, 08/659,683, 08/818,111, 08/818,112, 08/942,341, 08/942,578, 08/858,998, 08/859,381, 09/056,556, 09/072,596, 09/072,967, 09/073,009, 09/073,010, 09/223,040, 09/287,849, 09/597,796; and in PCT patent applications PCT/US00/28095; PCT/US98/10407, PCT/US98/10514, PCT/US99/03265, PCT/US99/03268, PCT/US99/07717, WO97/09428 and WO97/09429, WO98/16645, WO98/16646, each of which is herein incorporated by reference.

[0062] The antigens described herein include polymorphic variants and conservatively modified variations, as well as inter-strain and interspecies Mycobacterium homologs. In addition, the antigens described herein include subsequences or truncated sequences. The fusion proteins may also contain additional polypeptides, optionally heterologous peptides from Mycobacterium or other sources. These antigens may be modified, for example, by adding linker peptide sequences as described below. These linker peptides may be inserted between one or more polypeptides which make up each of the fusion proteins.

[0063] Definitions

[0064] “Fusion polypeptide” or “fusion protein” refers to a protein having at least two heterologous Mycobacterium sp. polypeptides covalently linked, either directly or via an amino acid linker. The polypeptides forming the fusion protein are typically linked C-terminus to N-terminus, although they can also be linked C-terminus to C-terminus, N-terminus to N-terminus, or N-terminus to C-terminus. The polypeptides of the fusion protein can be in any order. This term also refers to conservatively modified variants, polymorphic variants, alleles, mutants, subsequences, interspecies homologs, and immunogenic fragments of the antigens that make up the fusion protein. Mycobacterium tuberculosis antigens are described in Cole et al., Nature 393:537 (1998), which discloses the entire Mycobacterium tuberculosis genome. The complete sequence of Mycobacterium tuberculosis can also be found at http://www.sanger.ac.uk and at http://www.pasteur.fr/mycdb/(MycDB). Antigens from other Mycobacterium species that correspond to M. tuberculosis antigens can be identified, e.g., using sequence comparison algorithms, as described herein, or other methods known to those of skill in the art, e.g., hybridization assays and antibody binding assays. Fusion proteins of the invention can also comprise additional copies of a component antigen or immunogenic fragment thereof.

[0065] A polynucleotide sequence comprising a fusion protein of the invention hybridizes under stringent conditions to at least two nucleotide sequences, each encoding an antigen polypeptide selected from the group consisting of MTB39 or an immunogenic fragment thereof and MTB32A or an immunogenic fragment thereof. The polynucleotide sequences encoding the individual antigens of the fusion polypeptide therefore include conservatively modified variants, polymorphic variants, alleles, mutants, subsequences, immunogenic fragments, and interspecies homologs of MTB39 and MTB32A. The polynucleotide sequence encoding the individual polypeptides of the fusion protein can be in any order.

[0066] In some embodiments, the individual polypeptides of the fusion protein are in order (N- to C- terminus) from large to small. Large antigens are approximately 30 to 150 kD in size, medium antigens are approximately 10 to 30 kD in size, and small antigens are approximately less than 10 kD in size. The sequence encoding the individual polypeptide may be as small as, e.g., an immunogenic fragment such as an individual CTL epitope encoding about 8 to 9 amino acids, or, e.g., an HTL or B cell epitope. The fragment may also include multiple epitopes. The immunogenic fragment may also represent a larger part of the antigen sequence, e.g., about 50% or more of MTB39 and MTB32A, e.g., the N- and C-terminal portions of MTB32A. Preferred immunogenic fragments of MTB32A include Ra12, Ra35, and Ra35 MutSA.

[0067] A fusion polypeptide of the invention specifically binds to antibodies raised against at least two antigen polypeptides, wherein each antigen polypeptide is selected from the group consisting of MTB39 or an immunogenic portion or fragment thereof and MTB32A or an immunogenic portion thereof. The antibodies can be polyclonal or monoclonal. Optionally, the fusion polypeptide specifically binds to antibodies raised against the fusion junction of the antigens, which antibodies do not bind to the antigens individually, i.e., when they are not part of a fusion protein. The fusion polypeptides optionally comprise additional polypeptides, e.g., three, four, five, six, or more polypeptides, up to about 25 polypeptides, optionally heterologous polypeptides or repeated homologous polypeptides, fused to the at least two heterologous antigens. The additional polypeptides of the fusion protein are optionally derived from Mycobacterium as well as other sources, such as other bacterial, viral, or invertebrate, vertebrate, or mammalian sources. The individual polypeptides of the fusion protein can be in any order. As described herein, the fusion protein can also be linked to other molecules, including additional polypeptides. The compositions of the invention can also comprise additional polypeptides that are unlinked to the fusion proteins of the invention. These additional polypeptides may be heterologous or homologous polypeptides.

[0068] The term “fused” refers to the covalent linkage between two polypeptides in a fusion protein. The polypeptides are typically joined via a peptide bond, either directly to each other or via an amino acid linker. Optionally, the peptides can be joined via non-peptide covalent linkages known to those of skill in the art.

[0069] “FL” refers to full-length, i.e., a polypeptide that is the same length as the wild-type polypeptide.

[0070] The term “immunogenic fragment thereof” refers to a polypeptide comprising an epitope that is recognized by cytotoxic T lymphocytes, helper T lymphocytes or B cells. Preferred immunogenic fragments of, e.g., MTB32A, are RA35, Ra35MutSA, or Ra12.

[0071] The term “Mycobacterium species of the tuberculosis complex” includes those species traditionally considered as causing the disease tuberculosis, as well as Mycobacterium environmental and opportunistic species that cause tuberculosis and lung disease in immune compromised patients, such as patients with AIDS, e.g., M. tuberculosis, M bovis, or M. africanum, BCG, M avium, M intracellulare, M celatum, M. genavense, M. haemophilum, M. kansasii, M simiae, M. vaccae, M fortuitum, and M scrofulaceum (see, e.g., Harrison's Principles of Internal Medicine, volume 1, pp. 1004-1014 and 1019-1023 (14^(th) ed., Fauci et al., eds., 1998).

[0072] An adjuvant refers to the components in a vaccine or therapeutic composition that increase the specific immune response to the antigen (see, e.g., Edelman, AIDS Res. Hum Retroviruses 8:1409-1411 (1992)). Adjuvants induce immune responses of the Th1-type and Th-2 type response. Th1-type cytokines (e.g., IFN-γ, IL-2, and IL-12) tend to favor the induction of cell-mediated immune response to an administered antigen, while Th-2 type cytokines (e.g., IL-4, IL-5, Il-6, IL-10 and TNF-β) tend to favor the induction of humoral immune responses.

[0073] “Nucleic acid” refers to deoxyribonucleotides or ribonucleotides and polymers thereof in either single- or double-stranded form. The term encompasses nucleic acids containing known nucleotide analogs or modified backbone residues or linkages, which are synthetic, naturally occurring, and non-naturally occurring, which have similar binding properties as the reference nucleic acid, and which are metabolized in a manner similar to the reference nucleotides. Examples of such analogs include, without limitation, phosphorothioates, phosphoramidates, methyl phosphonates, chiral-methyl phosphonates, 2-O-methyl ribonucleotides, peptide-nucleic acids (PNAs).

[0074] Unless otherwise indicated, a particular nucleic acid sequence also implicitly encompasses conservatively modified variants thereof (e.g., degenerate codon substitutions) and complementary sequences, as well as the sequence explicitly indicated. Specifically, degenerate codon substitutions may be achieved by generating sequences in which the third position of one or more selected (or all) codons is substituted with mixed-base and/or deoxyinosine residues (Batzer et al., Nucleic Acid Res. 19:5081 (1991); Ohtsuka et al., J. Biol. Chem. 260:2605-2608 (1985); Rossolini et al., Mol. Cell. Probes 8:91-98 (1994)). The term nucleic acid is used interchangeably with gene, cDNA, mRNA, oligonucleotide, and polynucleotide.

[0075] The terms “polypeptide,” “peptide” and “protein” are used interchangeably herein to refer to a polymer of amino acid residues. The terms apply to amino acid polymers in which one or more amino acid residue is an artificial chemical mimetic of a corresponding naturally occurring amino acid, as well as to naturally occurring amino acid polymers and non-naturally occurring amino acid polymer.

[0076] The term “amino acid” refers to naturally occurring and synthetic amino acids, as well as amino acid analogs and amino acid mimetics that function in a manner similar to the naturally occurring amino acids. Naturally occurring amino acids are those encoded by the genetic code, as well as those amino acids that are later modified, e.g., hydroxyproline, γ-carboxyglutamate, and O-phosphoserine. Amino acid analogs refers to compounds that have the same basic chemical structure as a naturally occurring amino acid, i.e., an a carbon that is bound to a hydrogen, a carboxyl group, an amino group, and an R group, e.g., homoserine, norleucine, methionine sulfoxide, methionine methyl sulfonium. Such analogs have modified R groups (e.g., norleucine) or modified peptide backbones, but retain the same basic chemical structure as a naturally occurring amino acid. Amino acid mimetics refers to chemical compounds that have a structure that is different from the general chemical structure of an amino acid, but that functions in a manner similar to a naturally occurring amino acid.

[0077] Amino acids may be referred to herein by either their commonly known three letter symbols or by the one-letter symbols recommended by the IUPAC-IUB Biochemical Nomenclature Commission. Nucleotides, likewise, may be referred to by their commonly accepted single-letter codes.

[0078] “Conservatively modified variants” applies to both amino acid and nucleic acid sequences. With respect to particular nucleic acid sequences, conservatively modified variants refers to those nucleic acids which encode identical or essentially identical amino acid sequences, or where the nucleic acid does not encode an amino acid sequence, to essentially identical sequences. Because of the degeneracy of the genetic code, a large number of functionally identical nucleic acids encode any given protein. For instance, the codons GCA, GCC, GCG and GCU all encode the amino acid alanine. Thus, at every position where an alanine is specified by a codon, the codon can be altered to any of the corresponding codons described without altering the encoded polypeptide. Such nucleic acid variations are “silent variations,” which are one species of conservatively modified variations. Every nucleic acid sequence herein which encodes a polypeptide also describes every possible silent variation of the nucleic acid. One of skill will recognize that each codon in a nucleic acid (except AUG, which is ordinarily the only codon for methionine, and TGG, which is ordinarily the only codon for tryptophan) can be modified to yield a functionally identical molecule. Accordingly, each silent variation of a nucleic acid which encodes a polypeptide is implicit in each described sequence.

[0079] As to amino acid sequences, one of skill will recognize that individual substitutions, deletions or additions to a nucleic acid, peptide, polypeptide, or protein sequence which alters, adds or deletes a single amino acid or a small percentage of amino acids in the encoded sequence is a “conservatively modified variant” where the alteration results in the substitution of an amino acid with a chemically similar amino acid. Conservative substitution tables providing functionally similar amino acids are well known in the art. Such conservatively modified variants are in addition to and do not exclude polymorphic variants, interspecies homologs, and alleles of the invention.

[0080] The following eight groups each contain amino acids that are conservative substitutions for one another:

[0081] 1) Alanine (A), Glycine (G);

[0082] 2) Aspartic acid (D), Glutamic acid (E);

[0083] 3) Asparagine (N), Glutamine (Q);

[0084] 4) Arginine (R), Lysine (K);

[0085] 5) Isoleucine (I), Leucine (L), Methionine (M), Valine (V);

[0086] 6) Phenylalanine (F), Tyrosine (Y), Tryptophan (W);

[0087] 7) Serine (S), Threonine (T); and

[0088] 8) Cysteine (C), Methionine (M)

[0089] (see, e.g., Creighton, Proteins (1984)).

[0090] The term “heterologous” when used with reference to portions of a nucleic acid indicates that the nucleic acid comprises two or more subsequences that are not found in the same relationship to each other in nature. For instance, the nucleic acid is typically recombinantly produced, having two or more sequences from unrelated genes arranged to make a new functional nucleic acid, e.g., a promoter from one source and a coding region from another source. Similarly, a heterologous protein indicates that the protein comprises two or more subsequences that are not found in the same relationship to each other in nature (e.g., a fusion protein).

[0091] The phrase “selectively (or specifically) hybridizes to” refers to the binding, duplexing, or hybridizing of a molecule only to a particular nucleotide sequence under stringent hybridization conditions when that sequence is present in a complex mixture (e.g., total cellular or library DNA or RNA).

[0092] The phrase “stringent hybridization conditions” refers to conditions under which a probe will hybridize to its target subsequence, typically in a complex mixture of nucleic acid, but to no other sequences. Stringent conditions are sequence-dependent and will be different in different circumstances. Longer sequences hybridize specifically at higher temperatures. An extensive guide to the hybridization of nucleic acids is found in Tijssen, Techniques in Biochemistry and Molecular Biology—Hybridization with Nucleic Probes, “Overview of principles of hybridization and the strategy of nucleic acid assays” (1993). Generally, stringent conditions are selected to be about 5-10° C. lower than the thermal melting point (T_(m)) for the specific sequence at a defined ionic strength pH. The T_(m) is the temperature (under defined ionic strength, pH, and nucleic concentration) at which 50% of the probes complementary to the target hybridize to the target sequence at equilibrium (as the target sequences are present in excess, at T_(m), 50% of the probes are occupied at equilibrium). Stringent conditions will be those in which the salt concentration is less than about 1.0 M sodium ion, typically about 0.01 to 1.0 M sodium ion concentration (or other salts) at pH 7.0 to 8.3 and the temperature is at least about 30° C. for short probes (e.g., 10 to 50 nucleotides) and at least about 60° C. for long probes (e.g., greater than 50 nucleotides). Stringent conditions may also be achieved with the addition of destabilizing agents such as formamide. For selective or specific hybridization, a positive signal is at least two times background, optionally 10 times background hybridization. Exemplary stringent hybridization conditions can be as following: 50% formamide, 5× SSC, and 1% SDS, incubating at 42° C., or, 5× SSC, 1% SDS, incubating at 65° C., with wash in 0.2× SSC, and 0.1% SDS at 65° C.

[0093] Nucleic acids that do not hybridize to each other under stringent conditions are still substantially identical if the polypeptides which they encode are substantially identical. This occurs, for example, when a copy of a nucleic acid is created using the maximum codon degeneracy permitted by the genetic code. In such cases, the nucleic acids typically hybridize under moderately stringent hybridization conditions. Exemplary “moderately stringent hybridization conditions” include a hybridization in a buffer of 40% formamide, 1 M NaCl, 1% SDS at 37° C., and a wash in 1× SSC at 45° C. A positive hybridization is at least twice background. Those of ordinary skill will readily recognize that alternative hybridization and wash conditions can be utilized to provide conditions of similar stringency.

[0094] “Antibody” refers to a polypeptide comprising a framework region from an immunoglobulin gene or fragments thereof that specifically binds and recognizes an antigen. The recognized immunoglobulin genes include the kappa, lambda, alpha, gamma, delta, epsilon, and mu constant region genes, as well as the myriad immunoglobulin variable region genes. Light chains are classified as either kappa or lambda. Heavy chains are classified as gamma, mu, alpha, delta, or epsilon, which in turn define the immunoglobulin classes, IgG, IgM, IgA, IgD and IgE, respectively.

[0095] An exemplary immunoglobulin (antibody) structural unit comprises a tetramer. Each tetramer is composed of two identical pairs of polypeptide chains, each pair having one “light” (about 25 kDa) and one “heavy” chain (about 50-70 kDa). The N-terminus of each chain defines a variable region of about 100 to 110 or more amino acids primarily responsible for antigen recognition. The terms variable light chain (V_(L)) and variable heavy chain (V_(H)) refer to these light and heavy chains respectively.

[0096] Antibodies exist, e.g., as intact immunoglobulins or as a number of well-characterized fragments produced by digestion with various peptidases. Thus, for example, pepsin digests an antibody below the disulfide linkages in the hinge region to produce F(ab)′₂, a dimer of Fab which itself is a light chain joined to V_(H)-C_(H)1 by a disulfide bond. The F(ab)′₂ may be reduced under mild conditions to break the disulfide linkage in the hinge region, thereby converting the F(ab)′₂ dimer into an Fab′ monomer. The Fab′ monomer is essentially Fab with part of the hinge region (see Fundamental Immunology (Paul ed., 3d ed. 1993). While various antibody fragments are defined in terms of the digestion of an intact antibody, one of skill will appreciate that such fragments may be synthesized de novo either chemically or by using recombinant DNA methodology. Thus, the term antibody, as used herein, also includes antibody fragments either produced by the modification of whole antibodies, or those synthesized de novo using recombinant DNA methodologies (e.g., single chain Fv) or those identified using phage display libraries (see, e.g., McCafferty et al., Nature 348:552-554 (1990)).

[0097] For preparation of monoclonal or polyclonal antibodies, any technique known in the art can be used (see, e.g., Kohler & Milstein, Nature 256:495-497 (1975); Kozbor et al, Immunology Today 4: 72 (1983); Cole et al., pp. 77-96 in Monoclonal Antibodies and Cancer Therapy (1985)). Techniques for the production of single chain antibodies (U.S. Pat. No. 4,946,778) can be adapted to produce antibodies to polypeptides of this invention. Also, transgenic mice, or other organisms such as other mammals, may be used to express humanized antibodies. Alternatively, phage display technology can be used to identify antibodies and heteromeric Fab fragments that specifically bind to selected antigens (see, e.g., McCafferty et al., Nature 348:552-554 (1990); Marks et al., Biotechnology 10:779-783 (1992)).

[0098] The phrase “specifically (or selectively) binds” to an antibody or “specifically (or selectively) immunoreactive with,” when referring to a protein or peptide, refers to a binding reaction that is determinative of the presence of the protein in a heterogeneous population of proteins and other biologics. Thus, under designated immunoassay conditions, the specified antibodies bind to a particular protein at least two times the background and do not substantially bind in a significant amount to other proteins present in the sample. Specific binding to an antibody under such conditions may require an antibody that is selected for its specificity for a particular protein. For example, polyclonal antibodies raised to fusion proteins can be selected to obtain only those polyclonal antibodies that are specifically immunoreactive with fusion protein and not with individual components of the fusion proteins. This selection may be achieved by subtracting out antibodies that cross-react with the individual antigens. A variety of immunoassay formats may be used to select antibodies specifically immunoreactive with a particular protein. For example, solid-phase ELISA immunoassays are routinely used to select antibodies specifically immunoreactive with a protein (see, e.g., Harlow & Lane, Antibodies, A Laboratory Manual (1988), for a description of immunoassay formats and conditions that can be used to determine specific immunoreactivity). Typically a specific or selective reaction will be at least twice background signal or noise and more typically more than 10 to 100 times background.

[0099] Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes an individual antigen or a portion thereof) or may comprise a variant of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions such that the biological activity of the encoded fusion polypeptide is not diminished, relative to a fusion polypeptide comprising native antigens. Variants preferably exhibit at least about 70% identity, more preferably at least about 80% identity and most preferably at least about 90% identity to a polynucleotide sequence that encodes a native polypeptide or a portion thereof.

[0100] The terms “identical” or percent “identity,” in the context of two or more nucleic acids or polypeptide sequences, refer to two or more sequences or subsequences that are the same or have a specified percentage of amino acid residues or nucleotides that are the same (i.e., 70% identity, optionally 75%, 80%, 85%, 90%, or 95% identity over a specified region), when compared and aligned for maximum correspondence over a comparison window, or designated region as measured using one of the following sequence comparison algorithms or by manual alignment and visual inspection. Such sequences are then said to be “substantially identical.” This definition also refers to the compliment of a test sequence. Optionally, the identity exists over a region that is at least about 25 to about 50 amino acids or nucleotides in length, or optionally over a region that is 75-100 amino acids or nucleotides in length.

[0101] For sequence comparison, typically one sequence acts as a reference sequence, to which test sequences are compared. When using a sequence comparison algorithm, test and reference sequences are entered into a computer, subsequence coordinates are designated, if necessary, and sequence algorithm program parameters are designated. Default program parameters can be used, or alternative parameters can be designated. The sequence comparison algorithm then calculates the percent sequence identities for the test sequences relative to the reference sequence, based on the program parameters.

[0102] A “comparison window”, as used herein, includes reference to a segment of any one of the number of contiguous positions selected from the group consisting of from 25 to 500, usually about 50 to about 200, more usually about 100 to about 150 in which a sequence may be compared to a reference sequence of the same number of contiguous positions after the two sequences are optimally aligned. Methods of alignment of sequences for comparison are well-known in the art. Optimal alignment of sequences for comparison can be conducted, e.g., by the local homology algorithm of Smith & Waterman, Adv. Appl. Math. 2:482 (1981), by the homology alignment algorithm of Needleman & Wunsch, J. Mol Biol. 48:443 (1970), by the search for similarity method of Pearson & Lipman, Proc. Nat'l. Acad. Sci. USA 85:2444 (1988), by computerized implementations of these algorithms (GAP, BESTFIT, FASTA, and TFASTA in the Wisconsin Genetics Software Package, Genetics Computer Group, 575 Science Dr., Madison, Wis.), or by manual alignment and visual inspection (see, e.g., Current Protocols in Molecular Biology (Ausubel et al., eds. 1995 supplement)).

[0103] One example of a useful algorithm is PILEUP. PILEUP creates a multiple sequence alignment from a group of related sequences using progressive, pairwise alignments to show relationship and percent sequence identity. It also plots a tree or dendogram showing the clustering relationships used to create the alignment. PILEUP uses a simplification of the progressive alignment method of Feng & Doolittle, J. Mol. Evol. 35:351-360 (1987). The method used is similar to the method described by Higgins & Sharp, CABIOS 5:151-153 (1989). The program can align up to 300 sequences, each of a maximum length of 5,000 nucleotides or amino acids. The multiple alignment procedure begins with the pairwise alignment of the two most similar sequences, producing a cluster of two aligned sequences. This cluster is then aligned to the next most related sequence or cluster of aligned sequences. Two clusters of sequences are aligned by a simple extension of the pairwise alignment of two individual sequences. The final alignment is achieved by a series of progressive, pairwise alignments. The program is run by designating specific sequences and their amino acid or nucleotide coordinates for regions of sequence comparison and by designating the program parameters. Using PILEUP, a reference sequence is compared to other test sequences to determine the percent sequence identity relationship using the following parameters: default gap weight (3.00), default gap length weight (0.10), and weighted end gaps. PILEUP can be obtained from the GCG sequence analysis software package, e.g., version 7.0 (Devereaux et al., Nuc. Acids Res. 12:387-395 (1984).

[0104] Another example of algorithm that is suitable for determining percent sequence identity and sequence similarity are the BLAST and BLAST 2.0 algorithms, which are described in Altschul et al., Nuc. Acids Res. 25:3389-3402 (1977) and Altschul et al., J. Mol. Biol. 215:403-410 (1990), respectively. Software for performing BLAST analyses is publicly available through the National Center for Biotechnology Information (http://www.ncbi.nlm.nih.gov/). This algorithm involves first identifying high scoring sequence pairs (HSPs) by identifying short words of length W in the query sequence, which either match or satisfy some positive-valued threshold score T when aligned with a word of the same length in a database sequence. T is referred to as the neighborhood word score threshold (Altschul et al., supra). These initial neighborhood word hits act as seeds for initiating searches to find longer HSPs containing them. The word hits are extended in both directions along each sequence for as far as the cumulative alignment score can be increased. Cumulative scores are calculated using, for nucleotide sequences, the parameters M (reward score for a pair of matching residues; always >0) and N penalty score for mismatching residues; always <0). For amino acid sequences, a scoring matrix is used to calculate the cumulative score. Extension of the word hits in each direction are halted when: the cumulative alignment score falls off by the quantity X from its maximum achieved value; the cumulative score goes to zero or below, due to the accumulation of one or more negative-scoring residue alignments; or the end of either sequence is reached. The BLAST algorithm parameters W, T, and X determine the sensitivity and speed of the alignment. The BLASTN program (for nucleotide sequences) uses as defaults a wordlength (W) of 11, an expectation (E) or 10, M=5, N=−4 and a comparison of both strands. For amino acid sequences, the BLASTP program uses as defaults a wordlength of 3, and expectation (E) of 10, and the BLOSUM62 scoring matrix (see Henikoff & Henikoff, Proc. Natl. Acad. Sci. USA 89:10915 (1989)) alignments (B) of 50, expectation (E) of 10, M=5, N=−4, and a comparison of both strands.

[0105] The BLAST algorithm also performs a statistical analysis of the similarity between two sequences (see, e.g., Karlin & Altschul, Proc. Nat'l. Acad. Sci. USA 90:5873-5787 (1993)). One measure of similarity provided by the BLAST algorithm is the smallest sum probability (P(N)), which provides an indication of the probability by which a match between two nucleotide or amino acid sequences would occur by chance. For example, a nucleic acid is considered similar to a reference sequence if the smallest sum probability in a comparison of the test nucleic acid to the reference nucleic acid is less than about 0.2, more preferably less than about 0.01, and most preferably less than about 0.001.

[0106] Polynucleotide Compositions

[0107] As used herein, the terms “DNA segment” and “polynucleotide” refer to a DNA molecule that has been isolated free of total genomic DNA of a particular species. Therefore, a DNA segment encoding a polypeptide refers to a DNA segment that contains one or more coding sequences yet is substantially isolated away from, or purified free from, total genomic DNA of the species from which the DNA segment is obtained. Included within the terms “DNA segment” and “polynucleotide” are DNA segments and smaller fragments of such segments, and also recombinant vectors, including, for example, plasmids, cosmids, phagemids, phage, viruses, and the like.

[0108] As will be understood by those skilled in the art, the DNA segments of this invention can include genomic sequences, extra-genomic and plasmid-encoded sequences and smaller engineered gene segments that express, or may be adapted to express, proteins, polypeptides, peptides and the like. Such segments may be naturally isolated, or modified synthetically by the hand of man.

[0109] The terms “isolated,” “purified,” or “biologically pure” therefore refer to material that is substantially or essentially free from components that normally accompany it as found in its native state. Of course, this refers to the DNA segment as originally isolated, and does not exclude other isolated proteins, genes, or coding regions later added to the composition by the hand of man. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. An isolated nucleic acid is separated from other open reading frames that flank the gene and encode proteins other than the gene.

[0110] As will be recognized by the skilled artisan, polynucleotides may be single-stranded (coding or antisense) or double-stranded, and may be DNA (genomic, cDNA or synthetic) or RNA molecules. RNA molecules include HnRNA molecules, which contain introns and correspond to a DNA molecule in a one-to-one manner, and mRNA molecules, which do not contain introns. Additional coding or non-coding sequences may, but need not, be present within a polynucleotide of the present invention, and a polynucleotide may, but need not, be linked to other molecules and/or support materials.

[0111] Polynucleotides may comprise a native sequence (i.e., an endogenous sequence that encodes a Mycobacterium antigen or a portion thereof) or may comprise a variant, or a biological or antigenic functional equivalent of such a sequence. Polynucleotide variants may contain one or more substitutions, additions, deletions and/or insertions, as further described below, preferably such that the immunogenicity of the encoded polypeptide is not diminished, relative to a native tumor protein. The effect on the immunogenicity of the encoded polypeptide may generally be assessed as described herein. The term “variants” also encompasses homologous genes of xenogenic origin.

[0112] In additional embodiments, the present invention provides isolated polynucleotides and polypeptides comprising various lengths of contiguous stretches of sequence identical to or complementary to one or more of the sequences disclosed herein. For example, polynucleotides are provided by this invention that comprise at least about 15, 20, 30, 40, 50, 75, 100, 150, 200, 300, 400, 500 or 1000 or more contiguous nucleotides of one or more of the sequences disclosed herein as well as all intermediate lengths there between. It will be readily understood that “intermediate lengths”, in this context, means any length between the quoted values, such as 16, 17, 18, 19, etc.; 21, 22, 23, etc.; 30, 31, 32, etc.; 50, 51, 52, 53, etc.; 100, 101, 102, 103, etc.; 150, 151, 152, 153, etc.; including all integers through 200-500; 500-1,000, and the like.

[0113] The polynucleotides of the present invention, or fragments thereof, regardless of the length of the coding sequence itself, may be combined with other DNA sequences, such as promoters, polyadenylation signals, additional restriction enzyme sites, multiple cloning sites, other coding segments, and the like, such that their overall length may vary considerably. It is therefore contemplated that a nucleic acid fragment of almost any length may be employed, with the total length preferably being limited by the ease of preparation and use in the intended recombinant DNA protocol. For example, illustrative DNA segments with total lengths of about 10,000, about 5000, about 3000, about 2,000, about 1,000, about 500, about 200, about 100, about 50 base pairs in length, and the like, (including all intermediate lengths) are contemplated to be useful in many implementations of this invention.

[0114] Moreover, it will be appreciated by those of ordinary skill in the art that, as a result of the degeneracy of the genetic code, there are many nucleotide sequences that encode a polypeptide as described herein. Some of these polynucleotides bear minimal homology to the nucleotide sequence of any native gene. Nonetheless, polynucleotides that vary due to differences in codon usage are specifically contemplated by the present invention, for example polynucleotides that are optimized for human and/or primate codon selection. Further, alleles of the genes comprising the polynucleotide sequences provided herein are within the scope of the present invention. Alleles are endogenous genes that are altered as a result of one or more mutations, such as deletions, additions and/or substitutions of nucleotides. The resulting mRNA and protein may, but need not, have an altered structure or function. Alleles may be identified using standard techniques (such as hybridization, amplification and/or database sequence comparison).

[0115] Polynucleotide Identification and Characterization

[0116] Polynucleotides may be identified, prepared and/or manipulated using any of a variety of well established techniques. For example, a polynucleotide may be identified, as described in more detail below, by screening a microarray of cDNAs for tumor-associated expression (i.e., expression that is at least two fold greater in a tumor than in normal tissue, as determined using a representative assay provided herein). Such screens may be performed, for example, using a Synteni microarray (Palo Alto, Calif.) according to the manufacturer's instructions (and essentially as described by Schena et al., Proc. Natl. Acad. Sci. USA 93:10614-10619 (1996) and Heller et al., Proc. Natl. Acad. Sci. USA 94:2150-2155 (1997)). Alternatively, polynucleotides may be amplified from cDNA prepared from cells expressing the proteins described herein, such as M. tuberculosis cells. Such polynucleotides may be amplified via polymerase chain reaction (PCR). For this approach, sequence-specific primers may be designed based on the sequences provided herein, and may be purchased or synthesized.

[0117] An amplified portion of a polynucleotide of the present invention may be used to isolate a full length gene from a suitable library (e.g., a M tuberculosis cDNA library) using well known techniques. Within such techniques, a library (cDNA or genomic) is screened using one or more polynucleotide probes or primers suitable for amplification. Preferably, a library is size-selected to include larger molecules. Random primed libraries may also be preferred for identifying 5′ and upstream regions of genes. Genomic libraries are preferred for obtaining introns and extending 5′ sequences.

[0118] For hybridization techniques, a partial sequence may be labeled (e.g., by nick-translation or end-labeling with ³²P) using well known techniques. A bacterial or bacteriophage library is then generally screened by hybridizing filters containing denatured bacterial colonies (or lawns containing phage plaques) with the labeled probe (see Sambrook et al., Molecular Cloning: A Laboratory Manual (1989)). Hybridizing colonies or plaques are selected and expanded, and the DNA is isolated for further analysis. cDNA clones may be analyzed to determine the amount of additional sequence by, for example, PCR using a primer from the partial sequence and a primer from the vector. Restriction maps and partial sequences may be generated to identify one or more overlapping clones. The complete sequence may then be determined using standard techniques, which may involve generating a series of deletion clones. The resulting overlapping sequences can then assembled into a single contiguous sequence. A full length cDNA molecule can be generated by ligating suitable fragments, using well known techniques.

[0119] Alternatively, there are numerous amplification techniques for obtaining a full length coding sequence from a partial cDNA sequence. Within such techniques, amplification is generally performed via PCR. Any of a variety of commercially available kits may be used to perform the amplification step. Primers may be designed using, for example, software well known in the art. Primers are preferably 22-30 nucleotides in length, have a GC content of at least 50% and anneal to the target sequence at temperatures of about 68° C. to 72° C. The amplified region may be sequenced as described above, and overlapping sequences assembled into a contiguous sequence.

[0120] One such amplification technique is inverse PCR (see Triglia et al., Nucl. Acids Res. 16:8186 (1988)), which uses restriction enzymes to generate a fragment in the known region of the gene. The fragment is then circularized by intramolecular ligation and used as a template for PCR with divergent primers derived from the known region. Within an alternative approach, sequences adjacent to a partial sequence may be retrieved by amplification with a primer to a linker sequence and a primer specific to a known region. The amplified sequences are typically subjected to a second round of amplification with the same linker primer and a second primer specific to the known region. A variation on this procedure, which employs two primers that initiate extension in opposite directions from the known sequence, is described in WO 96/38591. Another such technique is known as “rapid amplification of cDNA ends” or RACE. This technique involves the use of an internal primer and an external primer, which hybridizes to a polyA region or vector sequence, to identify sequences that are 5′ and 3′ of a known sequence. Additional techniques include capture PCR (Lagerstrom et al., PCR Methods Applic. 1:111-19 (1991)) and walking PCR (Parker et al., Nucl. Acids. Res. 19:3055-60 (1991)). Other methods employing amplification may also be employed to obtain a full length cDNA sequence.

[0121] In certain instances, it is possible to obtain a full length cDNA sequence by analysis of sequences provided in an expressed sequence tag (EST) database, such as that available from GenBank. Searches for overlapping ESTs may generally be performed using well known programs (e.g., NCBI BLAST searches), and such ESTs may be used to generate a contiguous full length sequence. Full length DNA sequences may also be obtained by analysis of genomic fragments.

[0122] Polynucleotide Expression in Host Cells

[0123] In other embodiments of the invention, polynucleotide sequences or fragments thereof which encode polypeptides of the invention, or fusion proteins or functional equivalents thereof, may be used in recombinant DNA molecules to direct expression of a polypeptide in appropriate host cells. Due to the inherent degeneracy of the genetic code, other DNA sequences that encode substantially the same or a functionally equivalent amino acid sequence may be produced and these sequences may be used to clone and express a given polypeptide.

[0124] As will be understood by those of skill in the art, it may be advantageous in some instances to produce polypeptide-encoding nucleotide sequences possessing non-naturally occurring codons. For example, codons preferred by a particular prokaryotic or eukaryotic host can be selected to increase the rate of protein expression or to produce a recombinant RNA transcript having desirable properties, such as a half-life which is longer than that of a transcript generated from the naturally occurring sequence.

[0125] Moreover, the polynucleotide sequences of the present invention can be engineered using methods generally known in the art in order to alter polypeptide encoding sequences for a variety of reasons, including but not limited to, alterations which modify the cloning, processing, and/or expression of the gene product. For example, DNA shuffling by random fragmentation and PCR reassembly of gene fragments and synthetic oligonucleotides may be used to engineer the nucleotide sequences. In addition, site-directed mutagenesis may be used to insert new restriction sites, alter glycosylation patterns, change codon preference, produce splice variants, or introduce mutations, and so forth.

[0126] In another embodiment of the invention, natural, modified, or recombinant nucleic acid sequences may be ligated to a heterologous sequence to encode a fusion protein. For example, to screen peptide libraries for inhibitors of polypeptide activity, it may be useful to encode a chimeric protein that can be recognized by a commercially available antibody. A fusion protein may also be engineered to contain a cleavage site located between the polypeptide-encoding sequence and the heterologous protein sequence, so that the polypeptide may be cleaved and purified away from the heterologous moiety.

[0127] Sequences encoding a desired polypeptide may be synthesized, in whole or in part, using chemical methods well known in the art (see Caruthers, M. H. et al., Nucl. Acids Res. Symp. Ser. pp. 215-223 (1980), Horn et al, Nucl. Acids Res. Symp. Ser. pp. 225-232 (1980)). Alternatively, the protein itself may be produced using chemical methods to synthesize the amino acid sequence of a polypeptide, or a portion thereof. For example, peptide synthesis can be performed using various solid-phase techniques (Roberge et al., Science 269:202-204 (1995)) and automated synthesis may be achieved, for example, using the ABI 431A Peptide Synthesizer (Perkin Elmer, Palo Alto, Calif.).

[0128] A newly synthesized peptide may be substantially purified by preparative high performance liquid chromatography (e.g., Creighton, Proteins, Structures and Molecular Principles (1983)) or other comparable techniques available in the art. The composition of the synthetic peptides may be confirmed by amino acid analysis or sequencing (e.g., the Edman degradation procedure). Additionally, the amino acid sequence of a polypeptide, or any part thereof, may be altered during direct synthesis and/or combined using chemical methods with sequences from other proteins, or any part thereof, to produce a variant polypeptide.

[0129] In order to express a desired polypeptide, the nucleotide sequences encoding the polypeptide, or functional equivalents, may be inserted into appropriate expression vector, i.e., a vector which contains the necessary elements for the transcription and translation of the inserted coding sequence. Methods which are well known to those skilled in the art may be used to construct expression vectors containing sequences encoding a polypeptide of interest and appropriate transcriptional and translational control elements. These methods include in vitro recombinant DNA techniques, synthetic techniques, and in vivo genetic recombination. Such techniques are described in Sambrook et al., Molecular Cloning, A Laboratory Manual (1989), and Ausubel et al., Current Protocols in Molecular Biology (1989).

[0130] A variety of expression vector/host systems may be utilized to contain and express polynucleotide sequences. These include, but are not limited to, microorganisms such as bacteria transformed with recombinant bacteriophage, plasmid, or cosmid DNA expression vectors; yeast transformed with yeast expression vectors; insect cell systems infected with virus expression vectors (e.g., baculovirus); plant cell systems transformed with virus expression vectors (e.g., cauliflower mosaic virus, CaMV; tobacco mosaic virus, TMV) or with bacterial expression vectors (e.g., Ti or pBR322 plasmids); or animal cell systems.

[0131] The “control elements” or “regulatory sequences” present in an expression vector are those non-translated regions of the vector—enhancers, promoters, 5′ and 3′ untranslated regions—which interact with host cellular proteins to carry out transcription and translation. Such elements may vary in their strength and specificity. Depending on the vector system and host utilized, any number of suitable transcription and translation elements, including constitutive and inducible promoters, may be used. For example, when cloning in bacterial systems, inducible promoters such as the hybrid lacZ promoter of the PBLUESCRIPT phagemid (Stratagene, La Jolla, Calif.) or PSPORT1 plasmid (Gibco BRL, Gaithersburg, Md.) and the like may be used. In mammalian cell systems, promoters from mammalian genes or from mammalian viruses are generally preferred. If it is necessary to generate a cell line that contains multiple copies of the sequence encoding a polypeptide, vectors based on SV40 or EBV may be advantageously used with an appropriate selectable marker.

[0132] In bacterial systems, a number of expression vectors may be selected depending upon the use intended for the expressed polypeptide. For example, when large quantities are needed, for example for the induction of antibodies, vectors which direct high level expression of fusion proteins that are readily purified may be used. Such vectors include, but are not limited to, the multifunctional E. coli cloning and expression vectors such as BLUESCRIPT (Stratagene), in which the sequence encoding the polypeptide of interest may be ligated into the vector in frame with sequences for the amino-terminal Met and the subsequent 7 residues of β-galactosidase so that a hybrid protein is produced; pIN vectors (Van Heeke &Schuster, J. Biol. Chem. 264:5503-5509 (1989)); and the like. pGEX Vectors (Promega, Madison, Wis.) may also be used to express foreign polypeptides as fusion proteins with glutathione S-transferase (GST). In general, such fusion proteins are soluble and can easily be purified from lysed cells by adsorption to glutathione-agarose beads followed by elution in the presence of free glutathione. Proteins made in such systems may be designed to include heparin, thrombin, or factor XA protease cleavage sites so that the cloned polypeptide of interest can be released from the GST moiety at will.

[0133] In the yeast, Saccharomyces cerevisiae, a number of vectors containing constitutive or inducible promoters such as alpha factor, alcohol oxidase, and PGH may be used. For reviews, see Ausubel et al. (supra) and Grant et al., Methods Enzymol. 153:516-544 (1987).

[0134] In cases where plant expression vectors are used, the expression of sequences encoding polypeptides may be driven by any of a number of promoters. For example, viral promoters such as the 35S and 19S promoters of CaMV may be used alone or in combination with the omega leader sequence from TMV (Takamatsu, EMBO J. 6:307-311 (1987)). Alternatively, plant promoters such as the small subunit of RUBISCO or heat shock promoters may be used (Coruzzi et al., EMBO J. 3:1671-1680 (1984); Broglie et al., Science 224:838-843 (1984); and Winter et al., Results Probl. Cell Differ. 17:85-105 (1991)). These constructs can be introduced into plant cells by direct DNA transformation or pathogen-mediated transfection. Such techniques are described in a number of generally available reviews (see, e.g., Hobbs in McGraw Hill Yearbook of Science and Technology pp. 191-196 (1992)).

[0135] An insect system may also be used to express a polypeptide of interest. For example, in one such system, Autographa californica nuclear polyhedrosis virus (AcNPV) is used as a vector to express foreign genes in Spodoptera frugiperda cells or in Trichoplusia larvae. The sequences encoding the polypeptide may be cloned into a non-essential region of the virus, such as the polyhedrin gene, and placed under control of the polyhedrin promoter. Successful insertion of the polypeptide-encoding sequence will render the polyhedrin gene inactive and produce recombinant virus lacking coat protein. The recombinant viruses may then be used to infect, for example, S. frugiperda cells or Trichoplusia larvae in which the polypeptide of interest may be expressed (Engelhard et al., Proc. Natl. Acad. Sci. U.S.A. 91 :3224-3227 (1994)).

[0136] In mammalian host cells, a number of viral-based expression systems are generally available. For example, in cases where an adenovirus is used as an expression vector, sequences encoding a polypeptide of interest may be ligated into an adenovirus transcription/translation complex consisting of the late promoter and tripartite leader sequence. Insertion in a non-essential E1 or E3 region of the viral genome may be used to obtain a viable virus which is capable of expressing the polypeptide in infected host cells (Logan & Shenk, Proc. Natl. Acad. Sci. U.S.A. 81:3655-3659 (1984)). In addition, transcription enhancers, such as the Rous sarcoma virus (RSV) enhancer, may be used to increase expression in mammalian host cells.

[0137] Specific initiation signals may also be used to achieve more efficient translation of sequences encoding a polypeptide of interest. Such signals include the ATG initiation codon and adjacent sequences. In cases where sequences encoding the polypeptide, its initiation codon, and upstream sequences are inserted into the appropriate expression vector, no additional transcriptional or translational control signals may be needed. However, in cases where only coding sequence, or a portion thereof, is inserted, exogenous translational control signals including the ATG initiation codon should be provided. Furthermore, the initiation codon should be in the correct reading frame to ensure translation of the entire insert. Exogenous translational elements and initiation codons may be of various origins, both natural and synthetic. The efficiency of expression may be enhanced by the inclusion of enhancers which are appropriate for the particular cell system which is used, such as those described in the literature (Scharf. et al., Results Probl. Cell Differ. 20:125-162 (1994)).

[0138] In addition, a host cell strain may be chosen for its ability to modulate the expression of the inserted sequences or to process the expressed protein in the desired fashion. Such modifications of the polypeptide include, but are not limited to, acetylation, carboxylation. glycosylation, phosphorylation, lipidation, and acylation. Post-translational processing which cleaves a “prepro” form of the protein may also be used to facilitate correct insertion, folding and/or function. Different host cells such as CHO, HeLa, MDCK, HEK293, and W138, which have specific cellular machinery and characteristic mechanisms for such post-translational activities, may be chosen to ensure the correct modification and processing of the foreign protein.

[0139] For long-term, high-yield production of recombinant proteins, stable expression is generally preferred. For example, cell lines which stably express a polynucleotide of interest may be transformed using expression vectors which may contain viral origins of replication and/or endogenous expression elements and a selectable marker gene on the same or on a separate vector. Following the introduction of the vector, cells may be allowed to grow for 1-2 days in an enriched media before they are switched to selective media. The purpose of the selectable marker is to confer resistance to selection, and its presence allows growth and recovery of cells which successfully express the introduced sequences. Resistant clones of stably transformed cells may be proliferated using tissue culture techniques appropriate to the cell type.

[0140] Any number of selection systems may be used to recover transformed cell lines. These include, but are not limited to, the herpes simplex virus thymidine kinase (Wigler et al., Cell 11:223-32 (1977)) and adenine phosphoribosyltransferase (Lowy et al., Cell 22:817-23 (1990)) genes which can be employed in tk.sup.- or aprt.sup.- cells, respectively. Also, antimetabolite, antibiotic or herbicide resistance can be used as the basis for selection; for example, dhfr which confers resistance to methotrexate (Wigler et al., Proc. Natl. Acad. Sci. U.S.A. 77:3567-70 (1980)); npt, which confers resistance to the aminoglycosides, neomycin and G-418 (Colbere-Garapin et al., J. Mol. Biol. 150:1-14 (1981)); and als or pat, which confer resistance to chlorsulfuron and phosphinotricin acetyltransferase, respectively (Murry, supra). Additional selectable genes have been described, for example, trpB, which allows cells to utilize indole in place of tryptophan, or hisD, which allows cells to utilize histinol in place of histidine (Hartman & Mulligan, Proc. Natl. Acad. Sci. U.S.A. 85:8047-51 (1988)). Recently, the use of visible markers has gained popularity with such markers as anthocyanins, β-glucuronidase and its substrate GUS, and luciferase and its substrate luciferin, being widely used not only to identify transformants, but also to quantify the amount of transient or stable protein expression attributable to a specific vector system (Rhodes et al., Methods Mol. Biol. 55:121-131 (1995)).

[0141] Although the presence/absence of marker gene expression suggests that the gene of interest is also present, its presence and expression may need to be confirmed. For example, if the sequence encoding a polypeptide is inserted within a marker gene sequence, recombinant cells containing sequences can be identified by the absence of marker gene function. Alternatively, a marker gene can be placed in tandem with a polypeptide-encoding sequence under the control of a single promoter. Expression of the marker gene in response to induction or selection usually indicates expression of the tandem gene as well.

[0142] Alternatively, host cells which contain and express a desired polynucleotide sequence may be identified by a variety of procedures known to those of skill in the art. These procedures include, but are not limited to, DNA-DNA or DNA-RNA hybridizations and protein bioassay or immunoassay techniques which include membrane, solution, or chip based technologies for the detection and/or quantification of nucleic acid or protein.

[0143] A variety of protocols for detecting and measuring the expression of polynucleotide-encoded products, using either polyclonal or monoclonal antibodies specific for the product are known in the art. Examples include enzyme-linked immunosorbent assay (ELISA), radioimmunoassay (RIA), and fluorescence activated cell sorting (FACS). A two-site, monoclonal-based immunoassay utilizing monoclonal antibodies reactive to two non-interfering epitopes on a given polypeptide may be preferred for some applications, but a competitive binding assay may also be employed. These and other assays are described, among other places, in Hampton et al., Serological Methods, a Laboratory Manual (1990) and Maddox et al., J. Exp. Med. 158:1211-1216 (1983).

[0144] A wide variety of labels and conjugation techniques are known by those skilled in the art and may be used in various nucleic acid and amino acid assays. Means for producing labeled hybridization or PCR probes for detecting sequences related to polynucleotides include oligolabeling, nick translation, end-labeling or PCR amplification using a labeled nucleotide. Alternatively, the sequences, or any portions thereof may be cloned into a vector for the production of an mRNA probe. Such vectors are known in the art, are commercially available, and may be used to synthesize RNA probes in vitro by addition of an appropriate RNA polymerase such as T7, T3, or SP6 and labeled nucleotides. These procedures may be conducted using a variety of commercially available kits. Suitable reporter molecules or labels, which may be used include radionuclides, enzymes, fluorescent, chemiluminescent, or chromogenic agents as well as substrates, cofactors, inhibitors, magnetic particles, and the like.

[0145] Host cells transformed with a polynucleotide sequence of interest may be cultured under conditions suitable for the expression and recovery of the protein from cell culture. The protein produced by a recombinant cell may be secreted or contained intracellularly depending on the sequence and/or the vector used. As will be understood by those of skill in the art, expression vectors containing polynucleotides of the invention may be designed to contain signal sequences which direct secretion of the encoded polypeptide through a prokaryotic or eukaryotic cell membrane. Other recombinant constructions may be used to join sequences encoding a polypeptide of interest to nucleotide sequence encoding a polypeptide domain which will facilitate purification of soluble proteins. Such purification facilitating domains include, but are not limited to, metal chelating peptides such as histidine-tryptophan modules that allow purification on immobilized metals, protein A domains that allow purification on immobilized immunoglobulin, and the domain utilized in the FLAGS extension/affinity purification system (Immunex Corp., Seattle, Wash.). The inclusion of cleavable linker sequences such as those specific for Factor XA or enterokinase (Invitrogen. San Diego, Calif.) between the purification domain and the encoded polypeptide may be used to facilitate purification. One such expression vector provides for expression of a fusion protein containing a polypeptide of interest and a nucleic acid encoding 6 histidine residues preceding a thioredoxin or an enterokinase cleavage site. The histidine residues facilitate purification on IMIAC (immobilized metal ion affinity chromatography) as described in Porath et al., Prot. Exp. Purif. 3:263-281 (1992) while the enterokinase cleavage site provides a means for purifying the desired polypeptide from the fusion protein. A discussion of vectors which contain fusion proteins is provided in Kroll et al., DNA Cell Biol. 12:441-453 (1993)).

[0146] In addition to recombinant production methods, polypeptides of the invention, and fragments thereof, may be produced by direct peptide synthesis using solid-phase techniques (Merrifield, J. Am. Chem. Soc. 85:2149-2154 (1963)). Protein synthesis may be performed using manual techniques or by automation. Automated synthesis may be achieved, for example, using Applied Biosystems 431A Peptide Synthesizer (Perkin Elmer). Alternatively, various fragments may be chemically synthesized separately and combined using chemical methods to produce the full length molecule.

[0147] In Vivo Polynucleotide Delivery Techniques

[0148] In additional embodiments, genetic constructs comprising one or more of the polynucleotides of the invention are introduced into cells in vivo. This may be achieved using any of a variety or well known approaches, several of which are outlined below for the purpose of illustration.

[0149] 1. Adenovirus

[0150] One of the preferred methods for in vivo delivery of one or more nucleic acid sequences involves the use of an adenovirus expression vector. “Adenovirus expression vector” is meant to include those constructs containing adenovirus sequences sufficient to (a) support packaging of the construct and (b) to express a polynucleotide that has been cloned therein in a sense or antisense orientation. Of course, in the context of an antisense construct, expression does not require that the gene product be synthesized.

[0151] The expression vector comprises a genetically engineered form of an adenovirus. Knowledge of the genetic organization of adenovirus, a 36 kb, linear, double-stranded DNA virus, allows substitution of large pieces of adenoviral DNA with foreign sequences up to 7 kb (Grunhaus & Horwitz, 1992). In contrast to retrovirus, the adenoviral infection of host cells does not result in chromosomal integration because adenoviral DNA can replicate in an episomal manner without potential genotoxicity. Also, adenoviruses are structurally stable, and no genome rearrangement has been detected after extensive amplification. Adenovirus can infect virtually all epithelial cells regardless of their cell cycle stage. So far, adenoviral infection appears to be linked only to mild disease such as acute respiratory disease in humans.

[0152] Adenovirus is particularly suitable for use as a gene transfer vector because of its mid-sized genome, ease of manipulation, high titer, wide target-cell range and high infectivity. Both ends of the viral genome contain 100-200 base pair inverted repeats (ITRs), which are cis elements necessary for viral DNA replication and packaging. The early (E) and late (L) regions of the genome contain different transcription units that are divided by the onset of viral DNA replication. The E1 region (E1A and E1B) encodes proteins responsible for the regulation of transcription of the viral genome and a few cellular genes. The expression of the E2 region (E2A and E2B) results in the synthesis of the proteins for viral DNA replication. These proteins are involved in DNA replication, late gene expression and host cell shut-off (Renan, 1990). The products of the late genes, including the majority of the viral capsid proteins, are expressed only after significant processing of a single primary transcript issued by the major late promoter (MLP). The MLP, (located at 16.8 m.u.) is particularly efficient during the late phase of infection, and all the mRNA's issued from this promoter possess a 5′-tripartite leader (TPL) sequence which makes them preferred mRNA's for translation.

[0153] In a current system, recombinant adenovirus is generated from homologous recombination between shuttle vector and provirus vector. Due to the possible recombination between two proviral vectors, wild-type adenovirus may be generated from this process. Therefore, it is critical to isolate a single clone of virus from an individual plaque and examine its genomic structure.

[0154] Generation and propagation of the current adenovirus vectors, which are replication deficient, depend on a unique helper cell line, designated 293, which was transformed from human embryonic kidney cells by Ad5 DNA fragments and constitutively expresses E1 proteins (Graham et al, 1977). Since the E3 region is dispensable from the adenovirus genome (Jones & Shenk, 1978), the current adenovirus vectors, with the help of 293 cells, carry foreign DNA in either the E1, the D3 or both regions (Graham & Prevec, 1991). In nature, adenovirus can package approximately 105% of the wild-type genome (Ghosh-Choudhury et al., 1987), providing capacity for about 2 extra kB of DNA. Combined with the approximately 5.5 kB of DNA that is replaceable in the E1 and E3 regions, the maximum capacity of the current adenovirus vector is under 7.5 kB, or about 15% of the total length of the vector. More than 80% of the adenovirus viral genome remains in the vector backbone and is the source of vector-borne cytotoxicity. Also, the replication deficiency of the E1-deleted virus is incomplete. For example, leakage of viral gene expression has been observed with the currently available vectors at high multiplicities of infection (MOI) (Mulligan, 1993).

[0155] Helper cell lines may be derived from human cells such as human embryonic kidney cells, muscle cells, hematopoietic cells or other human embryonic mesenchymal or epithelial cells. Alternatively, the helper cells may be derived from the cells of other mammalian species that are permissive for human adenovirus. Such cells include, e.g., Vero cells or other monkey embryonic mesenchymal or epithelial cells. As stated above, the currently preferred helper cell line is 293.

[0156] Recently, Racher et al. (1995) disclosed improved methods for culturing 293 cells and propagating adenovirus. In one format, natural cell aggregates are grown by inoculating individual cells into 1 liter siliconized spinner flasks (Techne, Cambridge, UK) containing 100-200 ml of medium. Following stirring at 40 rpm, the cell viability is estimated with trypan blue. In another format, Fibra-Cel microcarriers (Bibby Sterlin, Stone, UK) (5 g/l) is employed as follows. A cell inoculum, resuspended in 5 ml of medium, is added to the carrier (50 ml) in a 250 ml Erlenmeyer flask and left stationary, with occasional agitation, for 1 to 4 h. The medium is then replaced with 50 ml of fresh medium and shaking initiated. For virus production, cells are allowed to grow to about 80% confluence, after which time the medium is replaced (to 25% of the final volume) and adenovirus added at an MOI of 0.05. Cultures are left stationary overnight, following which the volume is increased to 100% and shaking commenced for another 72 h.

[0157] Other than the requirement that the adenovirus vector be replication defective, or at least conditionally defective, the nature of the adenovirus vector is not believed to be crucial to the successful practice of the invention. The adenovirus may be of any of the 42 different known serotypes or subgroups A-F. Adenovirus type 5 of subgroup C is the preferred starting material in order to obtain a conditional replication-defective adenovirus vector for use in the present invention, since Adenovirus type 5 is a human adenovirus about which a great deal of biochemical and genetic information is known, and it has historically been used for most constructions employing adenovirus as a vector.

[0158] As stated above, the typical vector according to the present invention is replication defective and will not have an adenovirus E1 region. Thus, it will be most convenient to introduce the polynucleotide encoding the gene of interest at the position from which the E1-coding sequences have been removed. However, the position of insertion of the construct within the adenovirus sequences is not critical to the invention. The polynucleotide encoding the gene of interest may also be inserted in lieu of the deleted E3 region in E3 replacement vectors as described by Karlsson et al. (1986) or in the E4 region where a helper cell line or helper virus complements the E4 defect.

[0159] Adenovirus is easy to grow and manipulate and exhibits broad host range in vitro and in vivo. This group of viruses can be obtained in high titers, e.g., 10⁹-10 plaque-forming units per ml, and they are highly infective. The life cycle of adenovirus does not require integration into the host cell genome. The foreign genes delivered by adenovirus vectors are episomal and, therefore, have low genotoxicity to host cells. No side effects have been reported in studies of vaccination with wild-type adenovirus (Couch et al., 1963; Top et al., 1971), demonstrating their safety and therapeutic potential as in vivo gene transfer vectors.

[0160] Adenovirus vectors have been used in eukaryotic gene expression (Levrero et al., 1991; Gomez-Foix et al., 1992) and vaccine development (Grunhaus & Horwitz, 1992; Graham & Prevec, 1992). Recently, animal studies suggested that recombinant adenovirus could be used for gene therapy (Stratford-Perricaudet & Perricaudet, 1991; Stratford-Perricaudet et al., 1990; Rich et al., 1993). Studies in administering recombinant adenovirus to different tissues include trachea instillation (Rosenfeld et al., 1991; Rosenfeld et al., 1992), muscle injection (Ragot et al., 1993), peripheral intravenous injections (Herz & Gerard, 1993) and stereotactic inoculation into the brain (Le Gal La Salle et al., 1993).

[0161] 2. Retroviruses

[0162] The retroviruses are a group of single-stranded RNA viruses characterized by an ability to convert their RNA to double-stranded DNA in infected cells by a process of reverse-transcription (Coffin, 1990). The resulting DNA then stably integrates into cellular chromosomes as a provirus and directs synthesis of viral proteins. The integration results in the retention of the viral gene sequences in the recipient cell and its descendants. The retroviral genome contains three genes, gag, pol, and env that code for capsid proteins, polymerase enzyme, and envelope components, respectively. A sequence found upstream from the gag gene contains a signal for packaging of the genome into virions. Two long terminal repeat (LTR) sequences are present at the 5′ and 3′ ends of the viral genome. These contain strong promoter and enhancer sequences and are also required for integration in the host cell genome (Coffin, 1990).

[0163] In order to construct a retroviral vector, a nucleic acid encoding one or more oligonucleotide or polynucleotide sequences of interest is inserted into the viral genome in the place of certain viral sequences to produce a virus that is replication-defective. In order to produce virions, a packaging cell line containing the gag, pol, and env genes but without the LTR and packaging components is constructed (Mann et al., 1983). When a recombinant plasmid containing a cDNA, together with the retroviral LTR and packaging sequences is introduced into this cell line (by calcium phosphate precipitation for example), the packaging sequence allows the RNA transcript of the recombinant plasmid to be packaged into viral particles, which are then secreted into the culture media (Nicolas & Rubenstein, 1988; Temin, 1986; Mann et al., 1983). The media containing the recombinant retroviruses is then collected, optionally concentrated, and used for gene transfer. Retroviral vectors are able to infect a broad variety of cell types. However, integration and stable expression require the division of host cells (Paskind et al., 1975).

[0164] A novel approach designed to allow specific targeting of retrovirus vectors was recently developed based on the chemical modification of a retrovirus by the chemical addition of lactose residues to the viral envelope. This modification could permit the specific infection of hepatocytes via sialoglycoprotein receptors.

[0165] A different approach to targeting of recombinant retroviruses was designed in which biotinylated antibodies against a retroviral envelope protein and against a specific cell receptor were used. The antibodies were coupled via the biotin components by using streptavidin (Roux et al., 1989). Using antibodies against major histocompatibility complex class I and class II antigens, they demonstrated the infection of a variety of human cells that bore those surface antigens with an ecotropic virus in vitro (Roux et al., 1989).

[0166] 3. Adeno-Associated Viruses

[0167] AAV (Ridgeway, 1988; Hermonat & Muzycska, 1984) is a parovirus, discovered as a contamination of adenoviral stocks. It is a ubiquitous virus (antibodies are present in 85% of the US human population) that has not been linked to any disease. It is also classified as a dependovirus, because its replications is dependent on the presence of a helper virus, such as adenovirus. Five serotypes have been isolated, of which AAV-2 is the best characterized. AAV has a single-stranded linear DNA that is encapsidated into capsid proteins VP1, VP2 and VP3 to form an icosahedral virion of 20 to 24 nm in diameter (Muzyczka & McLaughlin, 1988).

[0168] The AAV DNA is approximately 4.7 kilobases long. It contains two open reading frames and is flanked by two ITRs. There are two major genes in the AAV genome: rep and cap. The rep gene codes for proteins responsible for viral replications, whereas cap codes for capsid protein VP1-3. Each ITR forms a T-shaped hairpin structure. These terminal repeats are the only essential cis components of the AAV for chromosomal integration. Therefore, the AAV can be used as a vector with all viral coding sequences removed and replaced by the cassette of genes for delivery. Three viral promoters have been identified and named p5, p 19, and p40, according to their map position. Transcription from p5 and p19 results in production of rep proteins, and transcription from p40 produces the capsid proteins (Hermonat & Muzyczka, 1984).

[0169] There are several factors that prompted researchers to study the possibility of using rAAV as an expression vector One is that the requirements for delivering a gene to integrate into the host chromosome are surprisingly few. It is necessary to have the 145-bp ITRs, which are only 6% of the AAV genome. This leaves room in the vector to assemble a 4.5-kb DNA insertion. While this carrying capacity may prevent the AAV from delivering large genes, it is amply suited for delivering the antisense constructs of the present invention.

[0170] AAV is also a good choice of delivery vehicles due to its safety. There is a relatively complicated rescue mechanism: not only wild type adenovirus but also AAV genes are required to mobilize rAAV. Likewise, AAV is not pathogenic and not associated with any disease. The removal of viral coding sequences minimizes immune reactions to viral gene expression, and therefore, rAAV does not evoke an inflammatory response. 4. Other Viral Vectors as Expression Constructs

[0171] Other viral vectors may be employed as expression constructs in the present invention for the delivery of oligonucleotide or polynucleotide sequences to a host cell. Vectors derived from viruses such as vaccinia virus (Ridgeway, 1988; Coupar et al., 1988), lentiviruses, polio viruses and herpes viruses may be employed. They offer several attractive features for various mammalian cells (Friedmann, 1989; Ridgeway, 1988; Coupar et al., 1988; Horwich et al., 1990).

[0172] With the recent recognition of defective hepatitis B viruses, new insight was gained into the structure-function relationship of different viral sequences. In vitro studies showed that the virus could retain the ability for helper-dependent packaging and reverse transcription despite the deletion of up to 80% of its genome (Horwich et al., 1990). This suggested that large portions of the genome could be replaced with foreign genetic material. The hepatotropism and persistence (integration) were particularly attractive properties for liver-directed gene transfer. Chang et al. (1991) introduced the chloramphenicol acetyltransferase (CAT) gene into duck hepatitis B virus genome in the place of the polymerase, surface, and pre-surface coding sequences. It was cotransfected with wild-type virus into an avian hepatoma cell line. Culture media containing high titers of the recombinant virus were used to infect primary duckling hepatocytes. Stable CAT gene expression was detected for at least 24 days after transfection (Chang et al., 1991).

[0173] 5. Non-Viral Vectors

[0174] In order to effect expression of the oligonucleotide or polynucleotide sequences of the present invention, the expression construct must be delivered into a cell. This delivery may be accomplished in vitro, as in laboratory procedures for transforming cells lines, or in vivo or ex vivo, as in the treatment of certain disease states. As described above, one preferred mechanism for delivery is via viral infection where the expression construct is encapsulated in an infectious viral particle.

[0175] Once the expression construct has been delivered into the cell the nucleic acid encoding the desired oligonucleotide or polynucleotide sequences may be positioned and expressed at different sites. In certain embodiments, the nucleic acid encoding the construct may be stably integrated into the genome of the cell. This integration may be in the specific location and orientation via homologous recombination (gene replacement) or it may be integrated in a random, non-specific location (gene augmentation). In yet further embodiments, the nucleic acid may be stably maintained in the cell as a separate, episomal segment of DNA. Such nucleic acid segments or “episomes” encode sequences sufficient to permit maintenance and replication independent of or in synchronization with the host cell cycle. How the expression construct is delivered to a cell and where in the cell the nucleic acid remains is dependent on the type of expression construct employed.

[0176] In certain embodiments of the invention, the expression construct comprising one or more oligonucleotide or polynucleotide sequences may simply consist of naked recombinant DNA or plasmids. Transfer of the construct may be performed by any of the methods mentioned above which physically or chemically permeabilize the cell membrane. This is particularly applicable for transfer in vitro but it may be applied to in vivo use as well. Dubensky et al. (1984) successfully injected polyomavirus DNA in the form of calcium phosphate precipitates into liver and spleen of adult and newborn mice demonstrating active viral replication and acute infection. Benvenisty & Reshef (1986) also demonstrated that direct intraperitoneal injection of calcium phosphate-precipitated plasmids results in expression of the transfected genes. It is envisioned that DNA encoding a gene of interest may also be transferred in a similar manner in vivo and express the gene product.

[0177] Another embodiment of the invention for transferring a naked DNA expression construct into cells may involve particle bombardment. This method depends on the ability to accelerate DNA-coated microprojectiles to a high velocity allowing them to pierce cell membranes and enter cells without killing them (Klein et al., 1987). Several devices for accelerating small particles have been developed. One such device relies on a high voltage discharge to generate an electrical current, which in turn provides the motive force (Yang et al., 1990). The microprojectiles used have consisted of biologically inert substances such as tungsten or gold beads.

[0178] Selected organs including the liver, skin, and muscle tissue of rats and mice have been bombarded in vivo (Yang et al., 1990; Zelenin et al., 1991). This may require surgical exposure of the tissue or cells, to eliminate any intervening tissue between the gun and the target organ, i.e., ex vivo treatment. Again, DNA encoding a particular gene may be delivered via this method and still be incorporated by the present invention.

[0179] Polypeptide Compositions

[0180] The present invention, in other aspects, provides polypeptide compositions. Generally, a polypeptide of the invention will be an isolated polypeptide (or an epitope, variant, or active fragment thereof) derived from a mammalian species. Preferably, the polypeptide is encoded by a polynucleotide sequence disclosed herein or a sequence which hybridizes under moderately stringent conditions to a polynucleotide sequence disclosed herein. Alternatively, the polypeptide may be defined as a polypeptide which comprises a contiguous amino acid sequence from an amino acid sequence disclosed herein, or which polypeptide comprises an entire amino acid sequence disclosed herein.

[0181] Immunogenic portions may generally be identified using well known techniques, such as those summarized in Paul, Fundamental Immunology, 3rd ed., 243-247 (1993) and references cited therein. Such techniques include screening polypeptides for the ability to react with antigen-specific antibodies, antisera and/or T-cell lines or clones. As used herein, antisera and antibodies are “antigen-specific” if they specifically bind to an antigen (i.e., they react with the protein in an ELISA or other immunoassay, and do not react detectably with unrelated proteins). Such antisera and antibodies may be prepared as described herein, and using well known techniques. An immunogenic portion of a Mycobacterium sp. protein is a portion that reacts with such antisera and/or T-cells at a level that is not substantially less than the reactivity of the full length polypeptide (e.g., in an ELISA and/or T-cell reactivity assay). Such immunogenic portions may react within such assays at a level that is similar to or greater than the reactivity of the full length polypeptide. Such screens may generally be performed using methods well known to those of ordinary skill in the art, such as those described in Harlow & Lane, Antibodies: A Laboratory Manual (1988). For example, a polypeptide may be immobilized on a solid support and contacted with patient sera to allow binding of antibodies within the sera to the immobilized polypeptide. Unbound sera may then be removed and bound antibodies detected using, for example, ¹²⁵I-labeled Protein A.

[0182] Polypeptides may be prepared using any of a variety of well known techniques. Recombinant polypeptides encoded by DNA sequences as described above may be readily prepared from the DNA sequences using any of a variety of expression vectors known to those of ordinary skill in the art. Expression may be achieved in any appropriate host cell that has been transformed or transfected with an expression vector containing a DNA molecule that encodes a recombinant polypeptide. Suitable host cells include prokaryotes, yeast, and higher eukaryotic cells, such as mammalian cells and plant cells. Preferably, the host cells employed are E. coli, yeast or a mammalian cell line such as COS or CHO. Supernatants from suitable host/vector systems which secrete recombinant protein or polypeptide into culture media may be first concentrated using a commercially available filter. Following concentration, the concentrate may be applied to a suitable purification matrix such as an affinity matrix or an ion exchange resin. Finally, one or more reverse phase HPLC steps can be employed to further purify a recombinant polypeptide.

[0183] Polypeptides of the invention, immunogenic fragments thereof, and other variant s having less than about 100 amino acids, and generally less than about 50 amino acids, may also be generated by synthetic means, using techniques well known to those of ordinary skill in the art. For example, such polypeptides may be synthesized using any of the commercially available solid-phase techniques, such as the Merrifield solid-phase synthesis method, where amino acids are sequentially added to a growing amino acid chain. See Merrifield, J Am. Chem. Soc. 85:2149-2146 (1963). Equipment for automated synthesis of polypeptides is commercially available from suppliers such as Perkin Elmer/Applied BioSystems Division (Foster City, Calif.), and may be operated according to the manufacturer's instructions.

[0184] Within certain specific embodiments, a polypeptide may be a fusion protein that comprises multiple polypeptides as described herein, or that comprises at least one polypeptide as described herein and an unrelated sequence, such as a known tumor protein. A fusion partner may, for example, assist in providing T helper epitopes (an immunological fusion partner), preferably T helper epitopes recognized by humans, or may assist in expressing the protein (an expression enhancer) at higher yields than the native recombinant protein. Certain preferred fusion partners are both immunological and expression enhancing fusion partners. Other fusion partners may be selected so as to increase the solubility of the protein or to enable the protein to be targeted to desired intracellular compartments. Still further fusion partners include affinity tags, which facilitate purification of the protein.

[0185] Fusion proteins may generally be prepared using standard techniques, including chemical conjugation. Preferably, a fusion protein is expressed as a recombinant protein, allowing the production of increased levels, relative to a non-fused protein, in an expression system. Briefly, DNA sequences encoding the polypeptide components may be assembled separately, and ligated into an appropriate expression vector. The 3′ end of the DNA sequence encoding one polypeptide component is ligated, with or without a peptide linker, to the 5′ end of a DNA sequence encoding the second polypeptide component so that the reading frames of the sequences are in phase. This permits translation into a single fusion protein that retains the biological activity of both component polypeptides.

[0186] A peptide linker sequence may be employed to separate the first and second polypeptide components by a distance sufficient to ensure that each polypeptide folds into its secondary and tertiary structures. Such a peptide linker sequence is incorporated into the fusion protein using standard techniques well known in the art. Suitable peptide linker sequences may be chosen based on the following factors: (1) their ability to adopt a flexible extended conformation; (2) their inability to adopt a secondary structure that could interact with functional epitopes on the first and second polypeptides; and (3) the lack of hydrophobic or charged residues that might react with the polypeptide functional epitopes. Preferred peptide linker sequences contain Gly, Asn and Ser residues. Other near neutral amino acids, such as Thr and Ala may also be used in the linker sequence. Amino acid sequences which may be usefully employed as linkers include those disclosed in Maratea et al., Gene 40:39-46 (1985); Murphy et al., Proc. Natl. Acad. Sci. USA 83:8258-8262 (1986); U.S. Pat. No. 4,935,233 and U.S. Pat. No. 4,751,180. The linker sequence may generally be from 1 to about 50 amino acids in length. Linker sequences are not required when the first and second polypeptides have non-essential N-terminal amino acid regions that can be used to separate the functional domains and prevent steric interference.

[0187] The ligated DNA sequences are operably linked to suitable transcriptional or translational regulatory elements. The regulatory elements responsible for expression of DNA are located only 5′ to the DNA sequence encoding the first polypeptides. Similarly, stop codons required to end translation and transcription termination signals are only present 3′ to the DNA sequence encoding the second polypeptide.

[0188] Fusion proteins are also provided. Such proteins comprise a polypeptide as described herein together with an unrelated immunogenic protein. Preferably the immunogenic protein is capable of eliciting a recall response. Examples of such proteins include tetanus, tuberculosis and hepatitis proteins (see, e.g., Stoute et al., New Engl. J. Med. 336:86-91 (1997)).

[0189] Within preferred embodiments, an immunological fusion partner is derived from protein D, a surface protein of the gram-negative bacterium Haemophilus influenza B (WO 91/18926). Preferably, a protein D derivative comprises approximately the first third of the protein (e.g., the first N-terminal 100-110 amino acids), and a protein D derivative may be lipidated. Within certain preferred embodiments, the first 109 residues of a lipoprotein D fusion partner is included on the N-terminus to provide the polypeptide with additional exogenous T-cell epitopes and to increase the expression level in E. coli (thus functioning as an expression enhancer). The lipid tail ensures optimal presentation of the antigen to antigen presenting cells. Other fusion partners include the non-structural protein from influenzae virus, NS1 (hemaglutinin). Typically, the N-terminal 81 amino acids are used, although different fragments that include T-helper epitopes may be used.

[0190] In another embodiment, the immunological fusion partner is the protein known as LYTA, or a portion thereof (preferably a C-terminal portion). LYTA is derived from Streptococcus pneumoniae, which synthesizes an N-acetyl-L-alanine amidase known as amidase LYTA (encoded by the LytA gene; Gene 43:265-292 (1986)). LYTA is an autolysin that specifically degrades certain bonds in the peptidoglycan backbone. The C-terminal domain of the LYTA protein is responsible for the affinity to the choline or to some choline analogues such as DEAE. This property has been exploited for the development of E. coli C-LYTA expressing plasmids useful for expression of fusion proteins. Purification of hybrid proteins containing the C-LYTA fragment at the amino terminus has been described (see Biotechnology 10:795-798 (1992)). Within a preferred embodiment, a repeat portion of LYTA may be incorporated into a fusion protein. A repeat portion is found in the C-terminal region starting at residue 178. A particularly preferred repeat portion incorporates residues 188-305.

[0191] In general, polypeptides (including fusion proteins) and polynucleotides as described herein are isolated. An “isolated” polypeptide or polynucleotide is one that is removed from its original environment. For example, a naturally-occurring protein is isolated if it is separated from some or all of the coexisting materials in the natural system. Preferably, such polypeptides are at least about 90% pure, more preferably at least about 95% pure and most preferably at least about 99% pure. A polynucleotide is considered to be isolated if, for example, it is cloned into a vector that is not a part of the natural environment.

[0192] T Cells

[0193] Immunotherapeutic compositions may also, or alternatively, comprise T cells specific for a Mycobacterium antigen. Such cells may generally be prepared in vitro or ex vivo, using standard procedures. For example, T cells may be isolated from bone marrow, peripheral blood, or a fraction of bone marrow or peripheral blood of a patient, using a commercially available cell separation system, such as the Isolex™ System, available from Nexell Therapeutics, Inc. (Irvine, Calif.; see also U.S. Pat. No. 5,240,856; U.S. Pat. No. 5,215,926; WO 89/06280; WO 91/16116 and WO 92/07243). Alternatively, T cells may be derived from related or unrelated humans, non-human mammals, cell lines or cultures.

[0194] T cells may be stimulated with a polypeptide of the invention, polynucleotide encoding such a polypeptide, and/or an antigen presenting cell (APC) that expresses such a polypeptide. Such stimulation is performed under conditions and for a time sufficient to permit the generation of T cells that are specific for the polypeptide. Preferably, the polypeptide or polynucleotide is present within a delivery vehicle, such as a microsphere, to facilitate the generation of specific T cells.

[0195] T cells are considered to be specific for a polypeptide of the invention if the T cells specifically proliferate, secrete cytokines or kill target cells coated with the polypeptide or expressing a gene encoding the polypeptide. T cell specificity may be evaluated using any of a variety of standard techniques. For example, within a chromium release assay or proliferation assay, a stimulation index of more than two fold increase in lysis and/or proliferation, compared to negative controls, indicates T cell specificity. Such assays may be performed, for example, as described in Chen et al., Cancer Res. 54:1065-1070 (1994)). Alternatively, detection of the proliferation of T cells may be accomplished by a variety of known techniques. For example, T cell proliferation can be detected by measuring an increased rate of DNA synthesis (e.g., by pulse-labeling cultures of T cells with tritiated thymidine and measuring the amount of tritiated thymidine incorporated into DNA). Contact with a polypeptide of the invention (100 ng/ml-100 μg/ml, preferably 200 ng/ml-25 μg/ml) for 3-7 days should result in at least a two fold increase in proliferation of the T cells. Contact as described above for 2-3 hours should result in activation of the T cells, as measured using standard cytokine assays in which a two fold increase in the level of cytokine release (e.g., TNF or IFN-γ) is indicative of T cell activation (see Coligan et al., Current Protocols in Immunology, vol. 1 (1998)). T cells that have been activated in response to a polypeptide, polynucleotide or polypeptide-expressing APC may be CD4⁺ and/or CD8⁺. Protein-specific T cells may be expanded using standard techniques. Within preferred embodiments, the T cells are derived from a patient, a related donor or an unrelated donor, and are administered to the patient following stimulation and expansion.

[0196] For therapeutic purposes, CD4⁺ or CD8⁺ T cells that proliferate in response to a polypeptide, polynucleotide or APC can be expanded in number either in vitro or in vivo. Proliferation of such T cells in vitro may be accomplished in a variety of ways. For example, the T cells can be re-exposed to a polypeptide, or a short peptide corresponding to an immunogenic portion of such a polypeptide, with or without the addition of T cell growth factors, such as interleukin-2, and/or stimulator cells that synthesize the polypeptide. Alternatively, one or more T cells that proliferate in the presence of the protein can be expanded in number by cloning. Methods for cloning cells are well known in the art, and include limiting dilution.

[0197] Pharmaceutical Compositions

[0198] In additional embodiments, the present invention concerns formulation of one or more of the polynucleotide, polypeptide, T-cell and/or antibody compositions disclosed herein in pharmaceutically-acceptable or physiologically-acceptable solutions for administration to a cell or an animal, either alone, or in combination with one or more other modalities of therapy. Such compositions are also useful for diagnostic uses.

[0199] It will also be understood that, if desired, the nucleic acid segment, RNA, DNA or PNA compositions that express a polypeptide as disclosed herein may be administered in combination with other agents as well, such as, e.g., other proteins or polypeptides or various pharmaceutically-active agents. In fact, there is virtually no limit to other components that may also be included, given that the additional agents do not cause a significant adverse effect upon contact with the target cells or host tissues. The compositions may thus be delivered along with various other agents as required in the particular instance. Such compositions may be purified from host cells or other biological sources, or alternatively may be chemically synthesized as described herein. Likewise, such compositions may further comprise substituted or derivatized RNA or DNA compositions.

[0200] Formulation of pharmaceutically-acceptable excipients and carrier solutions is well-known to those of skill in the art, as is the development of suitable dosing and treatment regimens for using the particular compositions described herein in a variety of treatment regimens, including e.g., oral, parenteral, intravenous, intranasal, and intramuscular administration and formulation.

[0201] 1. Oral Delivery

[0202] In certain applications, the pharmaceutical compositions disclosed herein may be delivered via oral administration to an animal. As such, these compositions may be formulated with an inert diluent or with an assimilable edible carrier, or they may be enclosed in hard- or soft-shell gelatin capsule, or they may be compressed into tablets, or they may be incorporated directly with the food of the diet.

[0203] The active compounds may even be incorporated with excipients and used in the form of ingestible tablets, buccal tables, troches, capsules, elixirs, suspensions, syrups, wafers, and the like (Mathiowitz et al., 1997; Hwang et al., 1998; U.S. Pat. No. 5,641,515; U.S. Pat. No. 5,580,579 and U.S. Pat. No. 5,792,451, each specifically incorporated herein by reference in its entirety). The tablets, troches, pills, capsules and the like may also contain the following: a binder, as gum tragacanth, acacia, cornstarch, or gelatin; excipients, such as dicalcium phosphate; a disintegrating agent, such as corn starch, potato starch, alginic acid and the like; a lubricant, such as magnesium stearate; and a sweetening agent, such as sucrose, lactose or saccharin may be added or a flavoring agent, such as peppermint, oil of wintergreen, or cherry flavoring. When the dosage unit form is a capsule, it may contain, in addition to materials of the above type, a liquid carrier. Various other materials may be present as coatings or to otherwise modify the physical form of the dosage unit. For instance, tablets, pills, or capsules may be coated with shellac, sugar, or both. A syrup of elixir may contain the active compound sucrose as a sweetening agent methyl and propylparabens as preservatives, a dye and flavoring, such as cherry or orange flavor. Of course, any material used in preparing any dosage unit form should be pharmaceutically pure and substantially non-toxic in the amounts employed. In addition, the active compounds may be incorporated into sustained-release preparation and formulations.

[0204] Typically, these formulations may contain at least about 0.1% of the active compound or more, although the percentage of the active ingredient(s) may, of course, be varied and may conveniently be between about 1 or 2% and about 60% or 70% or more of the weight or volume of the total formulation. Naturally, the amount of active compound(s) in each therapeutically useful composition may be prepared is such a way that a suitable dosage will be obtained in any given unit dose of the compound. Factors such as solubility, bioavailability, biological half-life, route of administration, product shelf life, as well as other pharmacological considerations will be contemplated by one skilled in the art of preparing such pharmaceutical formulations, and as such, a variety of dosages and treatment regimens may be desirable.

[0205] For oral administration the compositions of the present invention may alternatively be incorporated with one or more excipients in the form of a mouthwash, dentifrice, buccal tablet, oral spray, or sublingual orally-administered formulation. For example, a mouthwash may be prepared incorporating the active ingredient in the required amount in an appropriate solvent, such as a sodium borate solution (Dobell's Solution). Alternatively, the active ingredient may be incorporated into an oral solution such as one containing sodium borate, glycerin and potassium bicarbonate, or dispersed in a dentifrice, or added in a therapeutically-effective amount to a composition that may include water, binders, abrasives, flavoring agents, foaming agents, and humectants. Alternatively the compositions may be fashioned into a tablet or solution form that may be placed under the tongue or otherwise dissolved in the mouth.

[0206] 2. Injectable Delivery

[0207] In certain circumstances it will be desirable to deliver the pharmaceutical compositions disclosed herein parenterally, intravenously, intramuscularly, or even intraperitoneally as described in U.S. Pat. No. 5,543,158; U.S. Pat. No. 5,641,515 and U.S. Pat. No. 5,399,363 (each specifically incorporated herein by reference in its entirety). Solutions of the active compounds as free base or pharmacologically acceptable salts may be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions may also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms.

[0208] The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions (U.S. Pat. No. 5,466,468, specifically incorporated herein by reference in its entirety). In all cases the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. The carrier can be a solvent or dispersion medium containing, for example, water, ethanol, polyol (e.g., glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and/or vegetable oils. Proper fluidity may be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be facilitated by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminum monostearate and gelatin.

[0209] For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, a sterile aqueous medium that can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage may be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion (see, e.g., Remington's Pharmaceutical Sciences, 15th Edition, pp. 1035-1038 and 1570-1580). Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject. Moreover, for human administration, preparations should meet sterility, pyrogenicity, and the general safety and purity standards as required by FDA Office of Biologics standards.

[0210] Sterile injectable solutions are prepared by incorporating the active compounds in the required amount in the appropriate solvent with various of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof.

[0211] The compositions disclosed herein may be formulated in a neutral or salt form. Pharmaceutically-acceptable salts, include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms such as injectable solutions, drug-release capsules, and the like.

[0212] As used herein, “carrier” includes any and all solvents, dispersion media, vehicles, coatings, diluents, antibacterial and antifingal agents, isotonic and absorption delaying agents, buffers, carrier solutions, suspensions, colloids, and the like. The use of such media and agents for pharmaceutical active substances is well known in the art. Except insofar as any conventional media or agent is incompatible with the active ingredient, its use in the therapeutic compositions is contemplated. Supplementary active ingredients can also be incorporated into the compositions.

[0213] The phrase “pharmaceutically-acceptable” refers to molecular entities and compositions that do not produce an allergic or similar untoward reaction when administered to a human. The preparation of an aqueous composition that contains a protein as an active ingredient is well understood in the art. Typically, such compositions are prepared as injectables, either as liquid solutions or suspensions; solid forms suitable for solution in, or suspension in, liquid prior to injection can also be prepared. The preparation can also be emulsified.

[0214] 3. Nasal Delivery

[0215] In certain embodiments, the pharmaceutical compositions may be delivered by intranasal sprays, inhalation, and/or other aerosol delivery vehicles. Methods for delivering genes, nucleic acids, and peptide compositions directly to the lungs via nasal aerosol sprays has been described e.g., in U.S. Pat. No. 5,756,353 and U.S. Pat. No. 5,804,212 (each specifically incorporated herein by reference in its entirety). Likewise, the delivery of drugs using intranasal microparticle resins (Takenaga et al., 1998) and lysophosphatidyl-glycerol compounds (U.S. Pat. No. 5,725,871, specifically incorporated herein by reference in its entirety) are also well-known in the pharmaceutical arts. Likewise, transmucosal drug delivery in the form of a polytetrafluoroetheylene support matrix is described in U.S. Pat. No. 5,780,045 (specifically incorporated herein by reference in its entirety).

[0216] 4. Liposome-, Nanocapsule-, And Microparticle-Meda Ted Delivery

[0217] In certain embodiments, the inventors contemplate the use of liposomes, nanocapsules, microparticles, microspheres, lipid particles, vesicles, and the like, for the introduction of the compositions of the present invention into suitable host cells. In particular, the compositions of the present invention may be formulated for delivery either encapsulated in a lipid particle, a liposome, a vesicle, a nanosphere, or a nanoparticle or the like.

[0218] Such formulations may be preferred for the introduction of pharmaceutically-acceptable formulations of the nucleic acids or constructs disclosed herein. The formation and use of liposomes is generally known to those of skill in the art (see for example, Couvreur et al., 1977; Couvreur, 1988; Lasic, 1998; which describes the use of liposomes and nanocapsules in the targeted antibiotic therapy for intracellular bacterial infections and diseases). Recently, liposomes were developed with improved serum stability and circulation half-times (Gabizon & Papahadjopoulos, 1988; Allen and Choun, 1987; U.S. Pat. No. 5,741,516, specifically incorporated herein by reference in its entirety). Further, various methods of liposome and liposome like preparations as potential drug carriers have been reviewed (Takakura, 1998; Chandran et al., 1997; Margalit, 1995; U.S. Pat. No. 5,567,434; U.S. Pat. No. 5,552,157; U.S. Pat. No. 5,565,213; U.S. Pat. No. 5,738,868 and U.S. Pat. No. 5,795,587, each specifically incorporated herein by reference in its entirety).

[0219] Liposomes have been used successfully with a number of cell types that are normally resistant to transfection by other procedures including T cell suspensions, primary hepatocyte cultures and PC 12 cells (Renneisen et al., 1990; Muller et al., 1990). In addition, liposomes are free of the DNA length constraints that are typical of viral-based delivery systems. Liposomes have been used effectively to introduce genes, drugs (Heath & Martin, 1986; Heath et al., 1986; Balazsovits et al., 1989; Fresta & Puglisi, 1996), radiotherapeutic agents (Pikul et al, 1987), enzymes (Imaizumi et al., 1990a; Imaizumi et al., 1990b), viruses (Faller & Baltimore, 1984), transcription factors and allosteric effectors (Nicolau & Gersonde, 1979) into a variety of cultured cell lines and animals. In addition, several successful clinical trails examining the effectiveness of liposome-mediated drug delivery have been completed (Lopez-Berestein et al., 1985a; 1985b; Coune, 1988; Sculier et al., 1988). Furthermore, several studies suggest that the use of liposomes is not associated with autoimmune responses, toxicity or gonadal localization after systemic delivery (Mori & Fukatsu, 1992).

[0220] Liposomes are formed from phospholipids that are dispersed in an aqueous medium and spontaneously form multilamellar concentric bilayer vesicles (also termed multilamellar vesicles (MLVs). MLVs generally have diameters of from 25 nm to 4 μm. Sonication of MLVs results in the formation of small unilamellar vesicles (SUVs) with diameters in the range of 200 to 500 Å, containing an aqueous solution in the core.

[0221] Liposomes bear resemblance to cellular membranes and are contemplated for use in connection with the present invention as carriers for the peptide compositions. They are widely suitable as both water-and lipid-soluble substances can be entrapped, i.e. in the aqueous spaces and within the bilayer itself, respectively. It is possible that the drug-bearing liposomes may even be employed for site-specific delivery of active agents by selectively modifying the liposomal formulation.

[0222] In addition to the teachings of Couvreur et al. (1977; 1988), the following information may be utilized in generating liposomal formulations. Phospholipids can form a variety of structures other than liposomes when dispersed in water, depending on the molar ratio of lipid to water. At low ratios the liposome is the preferred structure. The physical characteristics of liposomes depend on pH, ionic strength and the presence of divalent cations. Liposomes can show low permeability to ionic and polar substances, but at elevated temperatures undergo a phase transition which markedly alters their permeability. The phase transition involves a change from a closely packed, ordered structure, known as the gel state, to a loosely packed, less-ordered structure, known as the fluid state. This occurs at a characteristic phase-transition temperature and results in an increase in permeability to ions, sugars and drugs.

[0223] In addition to temperature, exposure to proteins can alter the permeability of liposomes. Certain soluble proteins, such as cytochrome c, bind, deform and penetrate the bilayer, thereby causing changes in permeability. Cholesterol inhibits this penetration of proteins, apparently by packing the phospholipids more tightly. It is contemplated that the most useful liposome formations for antibiotic and inhibitor delivery will contain cholesterol.

[0224] The ability to trap solutes varies between different types of liposomes. For example, MLVs are moderately efficient at trapping solutes, but SUVs are extremely inefficient. SUVs offer the advantage of homogeneity and reproducibility in size distribution, however, and a compromise between size and trapping efficiency is offered by large unilamellar vesicles (LUVs). These are prepared by ether evaporation and are three to four times more efficient at solute entrapment than MLVs.

[0225] In addition to liposome characteristics, an important determinant in entrapping compounds is the physicochemical properties of the compound itself. Polar compounds are trapped in the aqueous spaces and nonpolar compounds bind to the lipid bilayer of the vesicle. Polar compounds are released through permeation or when the bilayer is broken, but nonpolar compounds remain affiliated with the bilayer unless it is disrupted by temperature or exposure to lipoproteins. Both types show maximum efflux rates at the phase transition temperature.

[0226] Liposomes interact with cells via four different mechanisms: endocytosis by phagocytic cells of the reticuloendothelial system such as macrophages and neutrophils; adsorption to the cell surface, either by nonspecific weak hydrophobic or electrostatic forces, or by specific interactions with cell-surface components; fusion with the plasma cell membrane by insertion of the lipid bilayer of the liposome into the plasma membrane, with simultaneous release of liposomal contents into the cytoplasm; and by transfer of liposomal lipids to cellular or subcellular membranes, or vice versa, without any association of the liposome contents. It often is difficult to determine which mechanism is operative and more than one may operate at the same time.

[0227] The fate and disposition of intravenously injected liposomes depend on their physical properties, such as size, fluidity, and surface charge. They may persist in tissues for h or days, depending on their composition, and half lives in the blood range from min to several h. Larger liposomes, such as MLVs and LUVs, are taken up rapidly by phagocytic cells of the reticuloendothelial system, but physiology of the circulatory system restrains the exit of such large species at most sites. They can exit only in places where large openings or pores exist in the capillary endothelium, such as the sinusoids of the liver or spleen. Thus, these organs are the predominate site of uptake. On the other hand, SUVs show a broader tissue distribution but still are sequestered highly in the liver and spleen. In general, this in vivo behavior limits the potential targeting of liposomes to only those organs and tissues accessible to their large size. These include the blood, liver, spleen, bone marrow, and lymphoid organs.

[0228] Targeting is generally not a limitation in terms of the present invention. However, should specific targeting be desired, methods are available for this to be accomplished. Antibodies may be used to bind to the liposome surface and to direct the antibody and its drug contents to specific antigenic receptors located on a particular cell-type surface. Carbohydrate determinants (glycoprotein or glycolipid cell-surface components that play a role in cell-cell recognition, interaction and adhesion) may also be used as recognition sites as they have potential in directing liposomes to particular cell types. Mostly, it is contemplated that intravenous injection of liposomal preparations would be used, but other routes of administration are also conceivable.

[0229] Alternatively, the invention provides for pharmaceutically-acceptable nanocapsule formulations of the compositions of the present invention. Nanocapsules can generally entrap compounds in a stable and reproducible way (Henry-Michelland et al, 1987; Quintanar-Guerrero et al., 1998; Douglas et al., 1987). To avoid side effects due to intracellular polymeric overloading, such ultrafine particles (sized around 0.1 μm) should be designed using polymers able to be degraded in vivo. Biodegradable polyalkyl-cyanoacrylate nanoparticles that meet these requirements are contemplated for use in the present invention. Such particles may be are easily made, as described (Couvreur et al., 1980; 1988; zur Muhlen et al., 1998; Zambaux et al. 1998; Pinto-Alphandry et al., 1995 and U.S. Pat. No. 5,145,684, specifically incorporated herein by reference in its entirety).

[0230] Vaccines

[0231] In certain preferred embodiments of the present invention, vaccines are provided. The vaccines will generally comprise one or more pharmaceutical compositions, such as those discussed above, in combination with an immunostimulant. An immunostimulant may be any substance that enhances or potentiates an immune response (antibody and/or cell-mediated) to an exogenous antigen. Examples of immunostimulants include adjuvants, biodegradable microspheres (e.g., polylactic galactide) and liposomes (into which the compound is incorporated; see, e.g., Fullerton, U.S. Pat. No. 4,235,877). Vaccine preparation is generally described in, for example, Powell & Newman, eds., Vaccine Design(the subunit and adjuvant approach) (1995). Pharmaceutical compositions and vaccines within the scope of the present invention may also contain other compounds, which may be biologically active or inactive. For example, one or more immunogenic portions of other tumor antigens may be present, either incorporated into a fusion polypeptide or as a separate compound, within the composition or vaccine.

[0232] Illustrative vaccines may contain DNA encoding one or more of the polypeptides as described above, such that the polypeptide is generated in situ. As noted above, the DNA may be present within any of a variety of delivery systems known to those of ordinary skill in the art, including nucleic acid expression systems, bacteria and viral expression systems. Numerous gene delivery techniques are well known in the art, such as those described by Rolland, Crit. Rev. Therap. Drug Carrier Systems 15:143-198 (1998), and references cited therein. Appropriate nucleic acid expression systems contain the necessary DNA sequences for expression in the patient (such as a suitable promoter and terminating signal). Bacterial delivery systems involve the administration of a bacterium (such as Bacillus-Calmette-Guerrin) that expresses an immunogenic portion of the polypeptide on its cell surface or secretes such an epitope. In a preferred embodiment, the DNA may be introduced using a viral expression system (e.g., vaccinia or other pox virus, retrovirus, or adenovirus), which may involve the use of a non-pathogenic (defective), replication competent virus. Suitable systems are disclosed, for example, in Fisher-Hoch et al., Proc. Natl. Acad. Sci. USA 86:317-321 (1989); Flexner et al., Ann. N.Y Acad. Sci. 569:86-103 (1989); Flexner et al, Vaccine 8:17-21 (1990); U.S. Pat. Nos. 4,603,112, 4,769,330, and 5,017,487; WO 89/01973; U.S. Pat. No. 4,777,127; GB 2,200,651; EP 0,345,242; WO 91/02805; Berkner, Biotechniques 6:616-627 (1988); Rosenfeld et al., Science 252:431-434 (1991); Kolls et al., Proc. Natl. Acad. Sci. USA 91:215-219 (1994); Kass-Eisler et al., Proc. Natl Acad. Sci. USA 90:11498-11502 (1993); Guzman et al., Circulation 88:2838-2848 (1993); and Guzman et al., Cir. Res. 73:1202-1207 (1993). Techniques for incorporating DNA into such expression systems are well known to those of ordinary skill in the art. The DNA may also be “naked,” as described, for example, in Ulmer et al., Science 259:1745-1749 (1993) and reviewed by Cohen, Science 259:1691-1692 (1993). The uptake of naked DNA may be increased by coating the DNA onto biodegradable beads, which are efficiently transported into the cells. It will be apparent that a vaccine may comprise both a polynucleotide and a polypeptide component. Such vaccines may provide for an enhanced immune response.

[0233] It will be apparent that a vaccine may contain pharmaceutically acceptable salts of the polynucleotides and polypeptides provided herein. Such salts may be prepared from pharmaceutically acceptable non-toxic bases, including organic bases (e.g., salts of primary, secondary and tertiary amines and basic amino acids) and inorganic bases (e.g., sodium, potassium, lithium, ammonium, calcium and magnesium salts).

[0234] While any suitable carrier known to those of ordinary skill in the art may be employed in the vaccine compositions of this invention, the type of carrier will vary depending on the mode of administration. Compositions of the present invention may be formulated for any appropriate manner of administration, including for example, topical, oral, nasal, intravenous, intracranial, intraperitoneal, subcutaneous or intramuscular administration. For parenteral administration, such as subcutaneous injection, the carrier preferably comprises water, saline, alcohol, a fat, a wax or a buffer. For oral administration, any of the above carriers or a solid carrier, such as mannitol, lactose, starch, magnesium stearate, sodium saccharine, talcum, cellulose, glucose, sucrose, and magnesium carbonate, may be employed. Biodegradable microspheres (e.g., polylactate polyglycolate) may also be employed as carriers for the pharmaceutical compositions of this invention. Suitable biodegradable microspheres are disclosed, for example, in U.S. Pat. Nos. 4,897,268; 5,075,109; 5,928,647; 5,811,128; 5,820,883; 5,853,763; 5,814,344 and 5,942,252. One may also employ a carrier comprising the particulate-protein complexes described in U.S. Pat. No. 5,928,647, which are capable of inducing a class I-restricted cytotoxic T lymphocyte responses in a host.

[0235] Such compositions may also comprise buffers (e.g., neutral buffered saline or phosphate buffered saline), carbohydrates (e.g., glucose, mannose, sucrose or dextrans), mannitol, proteins, polypeptides or amino acids such as glycine, antioxidants, bacteriostats, chelating agents such as EDTA or glutathione, adjuvants (e.g., aluminum hydroxide), solutes that render the formulation isotonic, hypotonic or weakly hypertonic with the blood of a recipient, suspending agents, thickening agents and/or preservatives. Alternatively, compositions of the present invention may be formulated as a lyophilizate. Compounds may also be encapsulated within liposomes using well known technology.

[0236] Any of a variety of immunostimulants may be employed in the vaccines of this invention. For example, an adjuvant may be included. Most adjuvants contain a substance designed to protect the antigen from rapid catabolism, such as aluminum hydroxide or mineral oil, and a stimulator of immune responses, such as lipid A, Bortadella pertussis or Mycobacterium species or Mycobacterium derived proteins. For example, delipidated, deglycolipidated M. vaccae(“pVac”) can be used. In another embodiment, BCG is used as an adjuvant. In addition, the vaccine can be administered to a subject previously exposed to BCG. Suitable adjuvants are commercially available as, for example, Freund's Incomplete Adjuvant and Complete Adjuvant (Difco Laboratories, Detroit, Mich.); Merck Adjuvant 65 (Merck and Company, Inc., Rahway, N.J.); AS-2 and derivatives thereof (SmithKline Beecham, Philadelphia, Pa.); CWS, TDM, Leif, aluminum salts such as aluminum hydroxide gel (alum) or aluminum phosphate; salts of calcium, iron or zinc; an insoluble suspension of acylated tyrosine; acylated sugars; cationically or anionically derivatized polysaccharides; polyphosphazenes; biodegradable microspheres; monophosphoryl lipid A and quil A. Cytokines, such as GM-CSF or interleukin-2, -7, or -12, may also be used as adjuvants.

[0237] Within the vaccines provided herein, the adjuvant composition is preferably designed to induce an immune response predominantly of the Th1 type. High levels of Th1-type cytokines (e.g., IFN-γ, TNFα, IL-2 and IL-12) tend to favor the induction of cell mediated immune responses to an administered antigen. In contrast, high levels of Th2-type cytokines (e.g., IL-4, IL-5, IL-6 and IL-10) tend to favor the induction of humoral immune responses. Following application of a vaccine as provided herein, a patient will support an immune response that includes Th1- and Th2-type responses. Within a preferred embodiment, in which a response is predominantly Th1-type, the level of Th1-type cytokines will increase to a greater extent than the level of Th2-type cytokines. The levels of these cytokines may be readily assessed using standard assays. For a review of the families of cytokines, see Mosmann & Coffman, Ann. Rev. Immunol. 7:145-173 (1989).

[0238] Preferred adjuvants for use in eliciting a predominantly Th1-type response include, for example, a combination of monophosphoryl lipid A, preferably 3-de-O-acylated monophosphoryl lipid A (3D-MPL), together with an aluminum salt. MPL adjuvants are available from Corixa Corporation (Seattle, Wash.; see U.S. Pat. Nos. 4,436,727; 4,877,611; 4,866,034 and 4,912,094). CpG-containing oligonucleotides (in which the CpG dinucleotide is unmethylated) also induce a predominantly Th1 response. Such oligonucleotides are well known and are described, for example, in WO 96/02555, WO 99/33488 and U.S. Pat. Nos. 6,008,200 and 5,856,462. Immunostimulatory DNA sequences are also described, for example, by Sato et al., Science 273:352 (1996). Another preferred adjuvant comprises a saponin, such as Quil A, or derivatives thereof, including QS21 and QS7 (Aquila Biopharmaceuticals Inc., Framingham, Mass.); Escin; Digitonin; or Gypsophila or Chenopodium quinoa saponins . Other preferred formulations include more than one saponin in the adjuvant combinations of the present invention, for example combinations of at least two of the following group comprising QS21, QS7, Quil A, β-escin, or digitonin.

[0239] Alternatively the saponin formulations may be combined with vaccine vehicles composed of chitosan or other polycationic polymers, polylactide and polylactide-co-glycolide particles, poly-N-acetyl glucosamine-based polymer matrix, particles composed of polysaccharides or chemically modified polysaccharides, liposomes and lipid-based particles, particles composed of glycerol monoesters, etc. The saponins may also be formulated in the presence of cholesterol to form particulate structures such as liposomes or ISCOMs. Furthermore, the saponins may be formulated together with a polyoxyethylene ether or ester, in either a non-particulate solution or suspension, or in a particulate structure such as a paucilamelar liposome or ISCOM. The saponins may also be formulated with excipients such as Carbopol^(R) to increase viscosity, or may be formulated in a dry powder form with a powder excipient such as lactose.

[0240] In one preferred embodiment, the adjuvant system includes the combination of a monophosphoryl lipid A and a saponin derivative, such as the combination of QS21 and 3D-MPL® adjuvant, as described in WO 94/00153, or a less reactogenic composition where the QS21 is quenched with cholesterol, as described in WO 96/33739. Other preferred formulations comprise an oil-in-water emulsion and tocopherol. Another particularly preferred adjuvant formulation employing QS21, 3D-MPL® adjuvant and tocopherol in an oil-in-water emulsion is described in WO 95/17210.

[0241] Another enhanced adjuvant system involves the combination of a CpG-containing oligonucleotide and a saponin derivative particularly the combination of CpG and QS21 as disclosed in WO 00/09159. Preferably the formulation additionally comprises an oil in water emulsion and tocopherol.

[0242] Other preferred adjuvants include Montanide ISA 720 (Seppic, France), SAF (Chiron, Calif., United States), ISCOMS (CSL), MF-59 (Chiron), the SBAS series of adjuvants (e.g., SBAS-2, AS2′, AS2,″ SBAS-4, or SBAS6, available from SmithKline Beecham, Rixensart, Belgium), Detox (Corixa, Hamilton, Mont.), RC-529 (Corixa, Hamilton, Mont.) and other aminoalkyl glucosaminide 4-phosphates (AGPs), such as those described in pending U.S. patent application Ser. Nos. 08/853,826 and 09/074,720, the disclosures of which are incorporated herein by reference in their entireties, and polyoxyethylene ether adjuvants such as those described in WO 99/52549A1.

[0243] Other preferred adjuvants include adjuvant molecules of the general formula (I):

HO(CH₂CH₂O)_(n)—A—R,

[0244] wherein, n is 1-50, A is a bond or —C(O)—, R is C₁₋₅₀ alkyl or Phenyl C₁₋₅₀ alkyl.

[0245] One embodiment of the present invention consists of a vaccine formulation comprising a polyoxyethylene ether of general formula (I), wherein n is between 1 and 50, preferably 4-24, most preferably 9; the R component is C₁₋₅₀, preferably C₄-C₂₀ alkyl and most preferably C₁₂ alkyl, and A is a bond. The concentration of the polyoxyethylene ethers should be in the range 0.1-20%, preferably from 0.1-10%, and most preferably in the range 0.1- 1%. Preferred polyoxyethylene ethers are selected from the following group: polyoxyethylene-9-lauryl ether, polyoxyethylene-9-steoryl ether, polyoxyethylene-8-steoryl ether, polyoxyethylene-4-lauryl ether, polyoxyethylene-35-lauryl ether, and polyoxyethylene-23-lauryl ether. Polyoxyethylene ethers such as polyoxyethylene lauryl ether are described in the Merck index (12^(th) edition: entry 7717). These adjuvant molecules are described in WO 99/52549.

[0246] The polyoxyethylene ether according to the general formula (I) above may, if desired, be combined with another adjuvant. For example, a preferred adjuvant combination is preferably with CpG as described in the pending UK patent application GB 9820956.2.

[0247] Any vaccine provided herein may be prepared using well known methods that result in a combination of antigen, immune response enhancer and a suitable carrier or excipient. The compositions described herein may be administered as part of a sustained release formulation (i.e., a formulation such as a capsule, sponge or gel (composed of polysaccharides, for example) that effects a slow release of compound following administration). Such formulations may generally be prepared using well known technology (see, e.g., Coombes et al., Vaccine 14:1429-1438 (1996)) and administered by, for example, oral, rectal or subcutaneous implantation, or by implantation at the desired target site. Sustained-release formulations may contain a polypeptide, polynucleotide or antibody dispersed in a carrier matrix and/or contained within a reservoir surrounded by a rate controlling membrane.

[0248] Carriers for use within such formulations are biocompatible, and may also be biodegradable; preferably the formulation provides a relatively constant level of active component release. Such carriers include microparticles of poly(lactide-co-glycolide), polyacrylate, latex, starch, cellulose, dextran and the like. Other delayed-release carriers include supramolecular biovectors, which comprise a non-liquid hydrophilic core (e.g., a cross-linked polysaccharide or oligosaccharide) and, optionally, an external layer comprising an amphiphilic compound, such as a phospholipid (see, e.g., U.S. Pat. No. 5,151,254 and PCT applications WO 94/20078, WO/94/23701 and WO 96/06638). The amount of active compound contained within a sustained release formulation depends upon the site of implantation, the rate and expected duration of release and the nature of the condition to be treated or prevented.

[0249] Any of a variety of delivery vehicles may be employed within pharmaceutical compositions and vaccines to facilitate production of an antigen-specific immune response that targets tumor cells. Delivery vehicles include antigen presenting cells (APCs), such as dendritic cells, macrophages, B cells, monocytes and other cells that may be engineered to be efficient APCs. Such cells may, but need not, be genetically modified to increase the capacity for presenting the antigen, to improve activation and/or maintenance of the T cell response, to have anti-tumor effects per se and/or to be immunologically compatible with the receiver (i.e., matched HLA haplotype). APCs may generally be isolated from any of a variety of biological fluids and organs, including tumor and peritumoral tissues, and may be autologous, allogeneic, syngeneic or xenogeneic cells.

[0250] Certain preferred embodiments of the present invention use dendritic cells or progenitors thereof as antigen-presenting cells. Dendritic cells are highly potent APCs (Banchereau & Steinman, Nature 392:245-251 (1998)) and have been shown to be effective as a physiological adjuvant for eliciting prophylactic or therapeutic antitumor immunity (see Timmerman & Levy, Ann. Rev. Med. 50:507-529 (1999)). In general, dendritic cells may be identified based on their typical shape (stellate in situ, with marked cytoplasmic processes (dendrites) visible in vitro), their ability to take up, process and present antigens with high efficiency and their ability to activate naive T cell responses. Dendritic cells may, of course, be engineered to express specific cell-surface receptors or ligands that are not commonly found on dendritic cells in vivo or ex vivo, and such modified dendritic cells are contemplated by the present invention. As an alternative to dendritic cells, secreted vesicles antigen-loaded dendritic cells (called exosomes) may be used within a vaccine (see Zitvogel et al., Nature Med. 4:594-600 (1998)).

[0251] Dendritic cells and progenitors may be obtained from peripheral blood, bone marrow, tumor-infiltrating cells, peritumoral tissues-infiltrating cells, lymph nodes, spleen, skin, umbilical cord blood or any other suitable tissue or fluid. For example, dendritic cells may be differentiated ex vivo by adding a combination of cytokines such as GM-CSF, IL-4, IL-13 and/or TNFα to cultures of monocytes harvested from peripheral blood. Alternatively, CD34 positive cells harvested from peripheral blood, umbilical cord blood or bone marrow may be differentiated into dendritic cells by adding to the culture medium combinations of GM-CSF, IL-3, TNFα , CD40 ligand, LPS, flt3 ligand and/or other compound(s) that induce differentiation, maturation and proliferation of dendritic cells.

[0252] Dendritic cells are conveniently categorized as “immature” and “mature” cells, which allows a simple way to discriminate between two well characterized phenotypes. However, this nomenclature should not be construed to exclude all possible intermediate stages of differentiation. Immature dendritic cells are characterized as APC with a high capacity for antigen uptake and processing, which correlates with the high expression of Fcγ receptor and mannose receptor. The mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e.g., CD54 and CD11) and costimulatory molecules (e.g., CD40, CD80, CD86 and 4-1BB).

[0253] APCs may generally be transfected with a polynucleotide encoding a protein (or portion or other variant thereof) such that the polypeptide, or an immunogenic portion thereof, is expressed on the cell surface. Such transfection may take place ex vivo, and a composition or vaccine comprising such transfected cells may then be used for therapeutic purposes, as described herein. Alternatively, a gene delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to a patient, resulting in transfection that occurs in vivo. In vivo and ex vivo transfection of dendritic cells, for example, may generally be performed using any methods known in the art, such as those described in WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and Cell Biology 75:456-460 (1997). Antigen loading of dendritic cells may be achieved by incubating dendritic cells or progenitor cells with the polypeptide, DNA (naked or within a plasmid vector) or RNA; or with antigen-expressing recombinant bacterium or viruses (e.g., vaccinia, fowlpox, adenovirus or lentivirus vectors). Prior to loading, the polypeptide may be covalently conjugated to an immunological partner that provides T cell help (e.g., a carrier molecule). Alternatively, a dendritic cell may be pulsed with a non-conjugated immunological partner, separately or in the presence of the polypeptide.

[0254] Vaccines and pharmaceutical compositions may be presented in unit-dose or multi-dose containers, such as sealed ampoules or vials. Such containers are preferably hermetically sealed to preserve sterility of the formulation until use. In general, formulations may be stored as suspensions, solutions or emulsions in oily or aqueous vehicles. Alternatively, a vaccine or pharmaceutical composition may be stored in a freeze-dried condition requiring only the addition of a sterile liquid carrier immediately prior to use.

[0255] Diagnostic Kits

[0256] The present invention further provides kits for use within any of the above diagnostic methods. Such kits typically comprise two or more components necessary for performing a diagnostic assay. Components may be compounds, reagents, containers and/or equipment. For example, one container within a kit may contain a monoclonal antibody or fragment thereof that specifically binds to a protein. Such antibodies or fragments may be provided attached to a support material, as described above. One or more additional containers may enclose elements, such as reagents or buffers, to be used in the assay. Such kits may also, or alternatively, contain a detection reagent as described above that contains a reporter group suitable for direct or indirect detection of antibody binding.

[0257] Alternatively, a kit may be designed to detect the level of mRNA encoding a protein in a biological sample. Such kits generally comprise at least one oligonucleotide probe or primer, as described above, that hybridizes to a polynucleotide encoding a protein. Such an oligonucleotide may be used, for example, within a PCR or hybridization assay. Additional components that may be present within such kits include a second oligonucleotide and/or a diagnostic reagent or container to facilitate the detection of a polynucleotide encoding a protein of the invention.

[0258] All publications and patent applications cited in this specification are herein incorporated by reference as if each individual publication or patent application were specifically and individually indicated to be incorporated by reference.

[0259] Although the foregoing invention has been described in some detail by way of illustration and example for purposes of clarity of understanding, it will be readily apparent to one of ordinary skill in the art in light of the teachings of this invention that certain changes and modifications may be made thereto without departing from the spirit or scope of the appended claims.

EXAMPLES

[0260] The following examples are provided by way of illustration only and not by way of limitation. Those of skill in the art will readily recognize a variety of noncritical parameters that could be changed or modified to yield essentially similar results.

Example 1 Guinea Pig Vaccination with MTB72F Fusion Protein and Compositions with Individual Antigens

[0261] Guinea pigs were immunized with adjuvant alone (SBAS1, SBAS2, or ASAS7 plus A1(OH)3), MTB72F fusion protein in adjuvant, or TbH9 plus Ra35 antigen composition.

[0262] Methods:

[0263] Groups: 1) SBAS1

[0264] 2) SBAS2

[0265] 3) SBAS7+A1(OH)3

[0266] 4) TbH9+Ra35+SBAS2

[0267] 5) TbH9+Ra35+SBAS2

[0268] 6) TbH9+Ra35+SBAS7(A1(OH)3)

[0269] 7) MTB72F in SBAS1

[0270] 8) MTB72F in SBAS2

[0271] 9) MTB72F in SBAS7+A1(OH)3

[0272] 10) PBS

[0273] 11) BCG

[0274] Dosage: 4 μg each of TbH9 and Ra35 8 μg MTB72F

[0275] Protocol: 1st immunization, 2nd immunization approximately 3 weeks later, 3rd immunization approximately two and a half weeks later.

[0276] Pre-challenge: DTH (delayed type hypersensitivity, used to determine antigenicity; 10 μg antigen)

[0277] Challenge: Aerosol with ˜30 cfu Erdman strain

[0278] Post challenge monitoring: Weight loss

[0279] Death (˜6 months post challenge)

[0280] Results:

[0281] 1. DTH

[0282] Positive reaction to the immunizing antigens. Reactions to individual antigens or the fusion protein were comparable. Skin test reactivity to PPD was only seen with the BCG immunized groups

[0283] 2. Protection: Guinea pigs vaccinated with MTB72F fusion protein afforded protection compared to those immunized with a mixture of antigens (see FIG. 1).

Example 2 Mouse Vaccination with MTB72F Fusion Protein and Compositions with Individual Antigens

[0284] As described above, mice were immunized with adjuvant alone (SBAS2, SBAS2′, SBAS2′, or SBAS6), MTB72F fusion protein in adjuvant, MTB72F DNA, MTB59F fusion protein in adjuvant, or TbH9, Ra35 and Ra12 antigen composition.

[0285] Methods:

[0286] Groups: 1) MTB72F+SBAS2

[0287] 2) MTB72F+SBAS2′

[0288] 3) MTB72F+SBAS2″

[0289] 4) MTB72F+SBAS6

[0290] 5) Ra12+TbH9+Ra35 in SBAS2

[0291] 6) MTB59F in SBAS2

[0292] 7) SBAS2

[0293] 8) MTB72F+delipidated, deglycolipidated M. vaccae

[0294] 9) MTB72F DNA

[0295] 10) MTB72F+IFA

[0296] 11) MTB72F+BCG

[0297] 12) delipidated, deglycolipidated M. vaccae

[0298] 13) BCG

[0299] 14) Saline

[0300] 15) MTB72F+SBAS2 (in house formulation)

[0301] 8 animals per group

[0302] Immunization schedule: First immunization, second immunization approximately 3 weeks later; third immunization approximately three weeks later.

[0303] Aerosol challenge approximately three months after first does

[0304] Spleen or lung cells were isolated and cultured; count CFU of cultures approximately three weeks after plating.

[0305] Dose: 8 μg MTB72F, 6.56 μg MTB59F, or 1.52, 4.3, and 2.24 μg, respectively, of Ra12, TbH9, and Ra35, mixed.

[0306] Results:

[0307] Of the AS adjuvants, AS2′+MTB72F gave the best protection in both the spleen and lung in this set of experiments (see FIGS. 2A and 2B). MTB72F gave ˜1 log better protection than MTB59F in both spleen and lung in this set of experiments, indicating that Ra12 provides additional benefit. Mixture of 12/H9/35+AS2 gave a better protection than MTB72F in this experiment. MTB72F DNA gave the best protection in this experiment, particularly in the spleen (>2 log). The protection was comparable in the lung to that seen with MTB72F protein+AS2″, in this experiment.

Example 3 Guinea Pig Vaccination with MTB72F Fusion Protein and Compositions with Individual Antigens

[0308] As described above, guinea pigs were immunized with adjuvant alone (SBAS2, SBAS2′, SBAS2″, or SBAS6), MTB72F fusion protein in adjuvant, MTB72F DNA, MTB59F fusion protein in adjuvant, or TbH9, Ra35 and Ra12 antigen composition.

[0309] Methods:

[0310] Groups: 1) MTB72F+SBAS2

[0311] 2) MTB72F+SBAS2′

[0312] 3) MTB72F+SBAS2″

[0313] 4) MTB72F+SBAS6

[0314] 5) Ra12+TbH9+Ra35 in SBAS2

[0315] 6) MTB59F in SBAS2

[0316] 7) SBAS2

[0317] 8) MTB72F+pvac

[0318] 9) MTB72F DNA

[0319] 10) MTB72F+IFA

[0320] 11) MTB72F+BCG

[0321] 12) BCG

[0322] 13) Saline

[0323] 14) delipidated, deglycolipidated M. vaccae

[0324] Antigens:

[0325] Antigens were formulated on a molar equivalent

[0326] 5 animals per group

[0327] Injection volume per dose is 250 μl (IM) containing MTB72F 20 μg Ra12, TbH9, Ra35 3.8, 10.8, and 5.6 μg MTB59F 16.4 μg Schedule:

[0328] 1 st immunization, 2nd immunization approximately three weeks later, 3rd immunization approximately three weeks later.

[0329] Challenge: ˜one and one half months after first immunization.

[0330] Results:

[0331] ˜38 Wks post challenge Groups Alive State G1. MTB72F + AS2 1/5 [losing weight] G2. MTB72F + AS2′ 2/5 [not gaining weight] G3. MTB72F + AS2″ 3/5 [looking okay, but no weight gain] G4. MTB72F + AS6 2/5 [both these gaining weight] G5. MTBRa12 + H9 + Ra35 + AS2 4/5 [one maybe a bit peaked, but two gaining] G6. MTB59F + AS2 2/5 [both losing a little] G7. AS2 2/5 [both losing] G8. MTB72F + pVac 1/5 [not looking too good] G9. MTB72F DNA 3/5 [all holding steady] G10. MTB72F + IFA 2/5 [doing okay] G11. MTB72F + BCG 5/5 [eating very well] G12 BCG 4/5 [doing fine] G13 Saline all dead G14 pVac 2/5 [not gaining weight]

[0332] By 50 weeks post challenge, while 80% (4/5 ) of the guinea pigs immunized with BCG+Mtb72F were still alive, only 20% (1/5) of those immunized with BCG alone were alive. At 85 weeks, 4/5 of the guinea pigs immunized with BCG+ Mtb72F were still alive and healthy (see FIG. 7).

Example 4 Long Term Protection

[0333] As described above, guinea pigs were immunized with adjuvant alone (AS2 or AS2″), MTB72F fusion protein in adjuvant, TbH9, Ra35 and Ra12 antigen composition, or a variety of individual antigens in adjuvant. Methods GROUPS ANTIGEN DOSE 1. AS2″ + MTB39 (TbH9) 20 ug/250 ul (IM) 2. AS2″ + MTB*.4 (DPV) 20 ug 3. AS2″ + MTB9.9 (MTI) 20 ug 4. AS2″ + MTB41 (MTCC#2) 20 ug 5. AS2″ + MTB40 (HTCC#1) 20 ug 6. AS2″ + MTB9.8 (MSL) 20 ug 7. AS2″ + MTB72F 20 ug 8. AS2″ + Ra12 + TbH9 + Ra35 (molar equivalent) 3.8 μg + 10.8 μg + 5.6 μg 9. AS2″ + MTB71F + MTB72F + HTCC#1 20 μg + 20 μg + 10 μg 10. AS2″ + Ra12 20 μg 11. BCG 12. AS2″ 13. AS2 + MTB72F 14. AS2 + Ra12 + TbH9 + Ra35 15. AS2

Example 5 Monkey Vaccination with MTB72F Fusion Protein and Compositions with Individual Antigens

[0334] As described above, monkeys were immunized with MTB72F fusion protein in SBAS2 adjuvant, or MTB8.4 antigen composition in adjuvant, or a mixture of MTB72F and MTB8.4.

[0335] Methods:

[0336] Groups

[0337] 1. Saline

[0338] 2. BCG

[0339] 3. MTB8.4/AS2

[0340] 4. MTB72F/AS2

[0341] 5. MTB72F/AS2 (one arm)+MTB8.4/AS2 (other arm)

[0342] 40 μg each antigen

[0343] Results:

[0344] At 8 weeks post challenge, monkeys immunized with BCG are showing signs of infection

[0345] Current data for 16 weeks post challenge reveals the following trend:

[0346] Groups immunized with MTB72F (4 and 5) are holding on their weights and have low ESR values compared to group 3 (MTB8.4 immunization) (Tables 1 and 2). TABLE 1 Prophylactic Vaccine Study in Cynomolgus Monkeys with MTB8.4 and MTB72F formulated in AS2 20 Weeks Post Challenge Net weight Groups ID Change (kg) Chest X-ray (onset) Status As2 1398K −24% Pn, bil, prog (wk 8) Alive 4437B −33% Pn, bil, prog (wk4) Dead 2959G −8.30% Pn, bil, prog (wk4) Alive 605AE −14.00% Pn, rt, stable (wk 8) Alive BCG 3436A −15.00% Neg Alive 3642G Plus 4.5% Pn, rt, prog (wk 8) Alive 1190H 0% Neg Alive 1051I −30% Pn, rt, prog (wk 8) Dead MTB8.4 3665C −25% Pn, rt, prog (wk8) Dead 2200F −18.00% Pn, rt, stable (wk8) Alive 1654J −33.00% Pn, bil, prog (wk4) Dead 4141C −33% Pn, bil, prog (wk4) Dead MTB72F 3061C* Died after IT challenge 1228G Plus 3.6% Bron, bil, stable for 3 mo (wk8) Alive 3462E −2.20% Neg Alive 4254C Plus 1.21 Pn, rt, stable for 3 mo (wk4) Alive MTB8.4 4496A Plus 7% Pn, rt, stable for 1 mo (wk 8) Alive MTB72F 4422C −39.00% Pn, bil, prog (wk 4) Dead 4416A Plus 11% Pn, rt, stable for 2 mo (wk 12) Alive 2734E Plus 12.5% Susp infil rt, stable for 3 mo (wk 8) Alive

[0347] TABLE 2 Prophylactic Vaccine Study in Cynomolgus Monkeys with MTB8.4 and MTB72F formulated in AS2 Wks Post Challenge ESR Groups ID 4 8 12 16 16 wks Chest X-ray AS2 1398K 3 3 10 19 Pn, bil, progrsv 4437B 10 20 3 Died 2959G 6 3 3 0 Pn, rt, progrsv 605AE 1 4 7 3 Pn, rt, stable BCG 3436A 0 8 7 15 Neg 3642G 0 0 0 0 Pn, rt, progrsv 1190H 1 0 2 0 Neg 1051I 0 8 22 7 Pn, bil, w/furt progrsn Died MTB8.4 3665C 12 30 19 Died 2200F 1 7 2 0 Pn, rt, progrsv 1654J 20 8 21 7 Pn, bil, w/fur progrsn 4141C 13 8 2 15 Pn, bil, w/fur progrsn MTB72F 3061C* Died after IT challenge 1228G 0 1 20 0 Now stable 3462E 0 0 0 0 Neg 4254C 13 0 0 0 Pn, now stable MTB8.4/ 4496A 5 1 0 5 Pn, rt, w/furt prog MTB72F 4422C 10 3 0 Died 4416A 6 0 1 0 Pn, now stable 2734E 0 0 0 0 Susp infil, now stable

Example 6 BCG Priming Experiment in Monkeys

[0348] 5 animals per group with four groups immunized with BCG and then rested, then immunized as described above and challenged. The following protocol will be used: Groups # animals Immunizing Antigen Antigen Dose 1. Nothing 5 AS2 2. BCG 5 AS2 3. BCG 5 MTB72F 40 ug 4. BCG 4 Ra12 + TbH9 + Ra35 Molar equiv of antigens in MTB72F dose 5. BCG 4 MTB72F + MTB71F + MTB40 40 ug MTB72F 40 ug MTB72F 20 ug MTB40

[0349] Antigens for T cell proliferation and cytokine Groups # animals Immunizing Antigen production assays 1. Nothing 5 AS2 PHA, PPD, MTB72F, MTB71F, HTCC#1, DPV, MTCC#2, Ra12, TbH9, Ra35, MSL, MTI 2. BCG 5 AS2 PHA, PPD, MTB72F, MTB71F, HTCC#1, DPV, MTCC#2, Ra12, TbH9, Ra35, MSL, MTI 3. BCG 5 MTB72F PHA, PPD, MTB72F, Ra12, TbH9, Ra35 4. BCG 4 Ra12 + TbH9 + Ra35 PHA, PPD, MTB72F, Ra12, TbH9, Ra35 5. BCG 4 MTB72F + MTB71F + MTB40 PHA, PPD, MTB72F, MTB71F, HTCC#1, DPV, MTCC-2, Ra12, TbH9, Ra35, MSL, MTI

Example 7 Construction of Ra35MutSA and MTB72FMutSA

[0350] Expression of Mtb72f typically results in some breakdown products. In addition, the expression of the full-length sequences of the mature or full length form of Ra35 (Mtb32A) in E. coli has been difficult. The expressed product was only visible after immunoblotting with a polyclonal rabbit anti-Ra35 Ab indicative of low levels of protein expression. Even then, multiple specific species (bands) were detected indicative of auto-catalytic breakdown (degradation) of the recombinant antigen. This was presumed to be due to the expression of Ra35FL in E. coli as a biologically active form.

[0351] It has been previously shown that it was possible to express Ra35FL as two overlapping halves comprising the N-terminal (Ra35N-term, called Ra35) and C-term halves (Ra35C-term called Ra12). To enhance and stabilize the expression of the whole Ra35 molecule, a single point mutation was introduced at one of the residues within the active-site triad (substitution of Ser to Ala; see FIGS. 6). This mutagenized form of Mtb32A can now be easily expressed at high levels in a stable form. In addition, to stabilize expression of Mtb72F, a single nucleotide substitution (T to G, resulting in a Ser to Ala change at position 710 of the fusion polypeptide) was incorporated in the sequence of Mtb72F at nucleotide position 2128 (see FIG. 5).

[0352] This stabilization is also readily accomplished by mutagenizing any one, any two, or all three of the three residues comprising the active site triad in Ra35FL, Ra35, or Mtb72F or other fusion proteins comprising Ra35 (His, Asp, or Ser). Mutagenesis can be performed using any technique known to one of skill in the art.

Example 8 Immunization of Mice withf Ra35FLMutSA-TbH9 and MTB72FMutSA

[0353] Eight mice per group were immunized with the compositions listed below, which include the adjuvant AS2A. The mice were then challenged with Mycobacterium tuberculosis, and survival of the mice was measured. Group Concentration of protein or DNA 1. Mtb72f protein 1.5 mg/ml 2. Mtb72f DNA 1.2 mg/ml 3. Mtb72f-85b protein 0.6 mg/ml 4. Mtb72f-85b DNA 1.1 mg/ml 5. Mtb72f-MTI protein 1.3 mg/ml 6. Mtb72f-MTI DNA 1.1 mg/ml 7. Mtb72fMutSA protein 1.7 mg/ml 8. MTB3AMutSA-TbH9 protein 2.4 mg/ml 9. BCG 10. AS2 11. vector alone 1.5 mg/ml 12. saline

[0354]

1 50 1 1872 DNA Mycobacterium tuberculosis MTB32A (Ra35FL) 1 gactacgttg gtgtagaaaa atcctgccgc ccggaccctt aaggctggga caatttctga 60 tagctacccc gacacaggag gttacgggat gagcaattcg cgccgccgct cactcaggtg 120 gtcatggttg ctgagcgtgc tggctgccgt cgggctgggc ctggccacgg cgccggccca 180 ggcggccccg ccggccttgt cgcaggaccg gttcgccgac ttccccgcgc tgcccctcga 240 cccgtccgcg atggtcgccc aagtggcgcc acaggtggtc aacatcaaca ccaaactggg 300 ctacaacaac gccgtgggcg ccgggaccgg catcgtcatc gatcccaacg gtgtcgtgct 360 gaccaacaac cacgtgatcg cgggcgccac cgacatcaat gcgttcagcg tcggctccgg 420 ccaaacctac ggcgtcgatg tggtcgggta tgaccgcacc caggatgtcg cggtgctgca 480 gctgcgcggt gccggtggcc tgccgtcggc ggcgatcggt ggcggcgtcg cggttggtga 540 gcccgtcgtc gcgatgggca acagcggtgg gcagggcgga acgccccgtg cggtgcctgg 600 cagggtggtc gcgctcggcc aaaccgtgca ggcgtcggat tcgctgaccg gtgccgaaga 660 gacattgaac gggttgatcc agttcgatgc cgcaatccag cccggtgatt cgggcgggcc 720 cgtcgtcaac ggcctaggac aggtggtcgg tatgaacacg gccgcgtccg ataacttcca 780 gctgtcccag ggtgggcagg gattcgccat tccgatcggg caggcgatgg cgatcgcggg 840 ccaaatccga tcgggtgggg ggtcacccac cgttcatatc gggcctaccg ccttcctcgg 900 cttgggtgtt gtcgacaaca acggcaacgg cgcacgagtc caacgcgtgg tcggaagcgc 960 tccggcggca agtctcggca tctccaccgg cgacgtgatc accgcggtcg acggcgctcc 1020 gatcaactcg gccaccgcga tggcggacgc gcttaacggg catcatcccg gtgacgtcat 1080 ctcggtgaac tggcaaacca agtcgggcgg cacgcgtaca gggaacgtga cattggccga 1140 gggacccccg gcctgatttg tcgcggatac cacccgccgg ccggccaatt ggattggcgc 1200 cagccgtgat tgccgcgtga gcccccgagt tccgtctccc gtgcgcgtgg cattgtggaa 1260 gcaatgaacg aggcagaaca cagcgttgag caccctcccg tgcagggcag ttacgtcgaa 1320 ggcggtgtgg tcgagcatcc ggatgccaag gacttcggca gcgccgccgc cctgcccgcc 1380 gatccgacct ggtttaagca cgccgtcttc tacgaggtgc tggtccgggc gttcttcgac 1440 gccagcgcgg acggttccgn cgatctgcgt ggactcatcg atcgcctcga ctacctgcag 1500 tggcttggca tcgactgcat ctgttgccgc cgttcctacg actcaccgct gcgcgacggc 1560 ggttacgaca ttcgcgactt ctacaaggtg ctgcccgaat tcggcaccgt cgacgatttc 1620 gtcgccctgg tcgacaccgc tcaccggcga ggtatccgca tcatcaccga cctggtgatg 1680 aatcacacct cggagtcgca cccctggttt caggagtccc gccgcgaccc agacggaccg 1740 tacggtgact attacgtgtg gagcgacacc agcgagcgct acaccgacgc ccggatcatc 1800 ttcgtcgaca ccgaagagtc gaactggtca ttcgatcctg tccgccgaca gttnctactg 1860 gcaccgattc tt 1872 2 355 PRT Mycobacterium tuberculosis MTB32A (Ra35FL) 2 Met Ser Asn Ser Arg Arg Arg Ser Leu Arg Trp Ser Trp Leu Leu Ser 1 5 10 15 Val Leu Ala Ala Val Gly Leu Gly Leu Ala Thr Ala Pro Ala Gln Ala 20 25 30 Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe Ala Asp Phe Pro Ala Leu 35 40 45 Pro Leu Asp Pro Ser Ala Met Val Ala Gln Val Ala Pro Gln Val Val 50 55 60 Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn Ala Val Gly Ala Gly Thr 65 70 75 80 Gly Ile Val Ile Asp Pro Asn Gly Val Val Leu Thr Asn Asn His Val 85 90 95 Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe Ser Val Gly Ser Gly Gln 100 105 110 Thr Tyr Gly Val Asp Val Val Gly Tyr Asp Arg Thr Gln Asp Val Ala 115 120 125 Val Leu Gln Leu Arg Gly Ala Gly Gly Leu Pro Ser Ala Ala Ile Gly 130 135 140 Gly Gly Val Ala Val Gly Glu Pro Val Val Ala Met Gly Asn Ser Gly 145 150 155 160 Gly Gln Gly Gly Thr Pro Arg Ala Val Pro Gly Arg Val Val Ala Leu 165 170 175 Gly Gln Thr Val Gln Ala Ser Asp Ser Leu Thr Gly Ala Glu Glu Thr 180 185 190 Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala Ile Gln Pro Gly Asp Ser 195 200 205 Gly Gly Pro Val Val Asn Gly Leu Gly Gln Val Val Gly Met Asn Thr 210 215 220 Ala Ala Ser Asp Asn Phe Gln Leu Ser Gln Gly Gly Gln Gly Phe Ala 225 230 235 240 Ile Pro Ile Gly Gln Ala Met Ala Ile Ala Gly Gln Ile Arg Ser Gly 245 250 255 Gly Gly Ser Pro Thr Val His Ile Gly Pro Thr Ala Phe Leu Gly Leu 260 265 270 Gly Val Val Asp Asn Asn Gly Asn Gly Ala Arg Val Gln Arg Val Val 275 280 285 Gly Ser Ala Pro Ala Ala Ser Leu Gly Ile Ser Thr Gly Asp Val Ile 290 295 300 Thr Ala Val Asp Gly Ala Pro Ile Asn Ser Ala Thr Ala Met Ala Asp 305 310 315 320 Ala Leu Asn Gly His His Pro Gly Asp Val Ile Ser Val Asn Trp Gln 325 330 335 Thr Lys Ser Gly Gly Thr Arg Thr Gly Asn Val Thr Leu Ala Glu Gly 340 345 350 Pro Pro Ala 355 3 1002 DNA Mycobacterium tuberculosis MTB32A (Ra35 mature) 3 catatgcatc accatcacca tcacgccccg ccggccttgt cgcaggaccg gttcgccgac 60 ttccccgcgc tgcccctcga cccgtccgcg atggtcgccc aagtggggcc acaggtggtc 120 aacatcaaca ccaaactggg ctacaacaac gccgtgggcg ccgggaccgg catcgtcatc 180 gatcccaacg gtgtcgtgct gaccaacaac cacgtgatcg cgggcgccac cgacatcaat 240 gcgttcagcg tcggctccgg ccaaacctac ggcgtcgatg tggtcgggta tgaccgcacc 300 caggatgtcg cggtgctgca gctgcgcggt gccggtggcc tgccgtcggc ggcgatcggt 360 ggcggcgtcg cggttggtga gcccgtcgtc gcgatgggca acagcggtgg gcagggcgga 420 acgccccgtg cggtgcctgg cagggtggtc gcgctcggcc aaaccgtgca ggcgtcggat 480 tcgctgaccg gtgccgaaga gacattgaac gggttgatcc agttcgatgc cgcgatccag 540 cccggtgagg cgggcgggcc cgtcgtcaac ggcctaggac aggtggtcgg tatgaacacg 600 gccgcgtccg ataacttcca gctgtcccag ggtgggcagg gattcgccat tccgatcggg 660 caggcgatgg cgatcgcggg ccagatccga tcgggtgggg ggtcacccac cgttcatatc 720 gggcctaccg ccttcctcgg cttgggtgtt gtcgacaaca acggcaacgg cgcacgagtc 780 caacgcgtgg tcgggagcgc tccggcggca agtctcggca tctccaccgg cgacgtgatc 840 accgcggtcg acggcgctcc gatcaactcg gccaccgcga tggcggacgc gcttaacggg 900 catcatcccg gtgacgtcat ctcggtgacc tggcaaacca agtcgggcgg cacgcgtaca 960 gggaacgtga cattggccga gggacccccg gcctgagaat tc 1002 4 330 PRT Mycobacterium tuberculosis MTB32A (Ra35 mature) 4 Met His His His His His His Ala Pro Pro Ala Leu Ser Gln Asp Arg 1 5 10 15 Phe Ala Asp Phe Pro Ala Leu Pro Leu Asp Pro Ser Ala Met Val Ala 20 25 30 Gln Val Gly Pro Gln Val Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn 35 40 45 Asn Ala Val Gly Ala Gly Thr Gly Ile Val Ile Asp Pro Asn Gly Val 50 55 60 Val Leu Thr Asn Asn His Val Ile Ala Gly Ala Thr Asp Ile Asn Ala 65 70 75 80 Phe Ser Val Gly Ser Gly Gln Thr Tyr Gly Val Asp Val Val Gly Tyr 85 90 95 Asp Arg Thr Gln Asp Val Ala Val Leu Gln Leu Arg Gly Ala Gly Gly 100 105 110 Leu Pro Ser Ala Ala Ile Gly Gly Gly Val Ala Val Gly Glu Pro Val 115 120 125 Val Ala Met Gly Asn Ser Gly Gly Gln Gly Gly Thr Pro Arg Ala Val 130 135 140 Pro Gly Arg Val Val Ala Leu Gly Gln Thr Val Gln Ala Ser Asp Ser 145 150 155 160 Leu Thr Gly Ala Glu Glu Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala 165 170 175 Ala Ile Gln Pro Gly Asp Ser Gly Gly Pro Val Val Asn Gly Leu Gly 180 185 190 Gln Val Val Gly Met Asn Thr Ala Ala Ser Asp Asn Phe Gln Leu Ser 195 200 205 Gln Gly Gly Gln Gly Phe Ala Ile Pro Ile Gly Gln Ala Met Ala Ile 210 215 220 Ala Gly Gln Ile Arg Ser Gly Gly Gly Ser Pro Thr Val His Ile Gly 225 230 235 240 Pro Thr Ala Phe Leu Gly Leu Gly Val Val Asp Asn Asn Gly Asn Gly 245 250 255 Ala Arg Val Gln Arg Val Val Gly Ser Ala Pro Ala Ala Ser Leu Gly 260 265 270 Ile Ser Thr Gly Asp Val Ile Thr Ala Val Asp Gly Ala Pro Ile Asn 275 280 285 Ser Ala Thr Ala Met Ala Asp Ala Leu Asn Gly His His Pro Gly Asp 290 295 300 Val Ile Ser Val Thr Trp Gln Thr Lys Ser Gly Gly Thr Arg Thr Gly 305 310 315 320 Asn Val Thr Leu Ala Glu Gly Pro Pro Ala 325 330 5 1002 DNA Artificial Sequence Description of Artificial SequenceRa35FLMutSA 5 catatgcatc accatcacca tcacgccccg ccggccttgt cgcaggaccg gttcgccgac 60 ttccccgcgc tgcccctcga cccgtccgcg atggtcgccc aagtggggcc acaggtggtc 120 aacatcaaca ccaaactggg ctacaacaac gccgtgggcg ccgggaccgg catcgtcatc 180 gatcccaacg gtgtcgtgct gaccaacaac cacgtgatcg cgggcgccac cgacatcaat 240 gcgttcagcg tcggctccgg ccaaacctac ggcgtcgatg tggtcgggta tgaccgcacc 300 caggatgtcg cggtgctgca gctgcgcggt gccggtggcc tgccgtcggc ggcgatcggt 360 ggcggcgtcg cggttggtga gcccgtcgtc gcgatgggca acagcggtgg gcagggcgga 420 acgccccgtg cggtgcctgg cagggtggtc gcgctcggcc aaaccgtgca ggcgtcggat 480 tcgctgaccg gtgccgaaga gacattgaac gggttgatcc agttcgatgc cgcgatccag 540 cccggtgatg cgggcgggcc cgtcgtcaac ggcctaggac aggtggtcgg tatgaacacg 600 gccgcgtccg ataacttcca gctgtcccag ggtgggcagg gattcgccat tccgatcggg 660 caggcgatgg cgatcgcggg ccagatccga tcgggtgggg ggtcacccac cgttcatatc 720 gggcctaccg ccttcctcgg cttgggtgtt gtcgacaaca acggcaacgg cgcacgagtc 780 caacgcgtgg tcgggagcgc tccggcggca agtctcggca tctccaccgg cgacgtgatc 840 accgcggtcg acggcgctcc gatcaactcg gccaccgcga tggcggacgc gcttaacggg 900 catcatcccg gtgacgtcat ctcggtgacc tggcaaacca agtcgggcgg cacgcgtaca 960 gggaacgtga cattggccga gggacccccg gcctgagaat tc 1002 6 330 PRT Artificial Sequence Description of Artificial SequenceRa35FLMutSA 6 Met His His His His His His Ala Pro Pro Ala Leu Ser Gln Asp Arg 1 5 10 15 Phe Ala Asp Phe Pro Ala Leu Pro Leu Asp Pro Ser Ala Met Val Ala 20 25 30 Gln Val Gly Pro Gln Val Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn 35 40 45 Asn Ala Val Gly Ala Gly Thr Gly Ile Val Ile Asp Pro Asn Gly Val 50 55 60 Val Leu Thr Asn Asn His Val Ile Ala Gly Ala Thr Asp Ile Asn Ala 65 70 75 80 Phe Ser Val Gly Ser Gly Gln Thr Tyr Gly Val Asp Val Val Gly Tyr 85 90 95 Asp Arg Thr Gln Asp Val Ala Val Leu Gln Leu Arg Gly Ala Gly Gly 100 105 110 Leu Pro Ser Ala Ala Ile Gly Gly Gly Val Ala Val Gly Glu Pro Val 115 120 125 Val Ala Met Gly Asn Ser Gly Gly Gln Gly Gly Thr Pro Arg Ala Val 130 135 140 Pro Gly Arg Val Val Ala Leu Gly Gln Thr Val Gln Ala Ser Asp Ser 145 150 155 160 Leu Thr Gly Ala Glu Glu Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala 165 170 175 Ala Ile Gln Pro Gly Asp Ala Gly Gly Pro Val Val Asn Gly Leu Gly 180 185 190 Gln Val Val Gly Met Asn Thr Ala Ala Ser Asp Asn Phe Gln Leu Ser 195 200 205 Gln Gly Gly Gln Gly Phe Ala Ile Pro Ile Gly Gln Ala Met Ala Ile 210 215 220 Ala Gly Gln Ile Arg Ser Gly Gly Gly Ser Pro Thr Val His Ile Gly 225 230 235 240 Pro Thr Ala Phe Leu Gly Leu Gly Val Val Asp Asn Asn Gly Asn Gly 245 250 255 Ala Arg Val Gln Arg Val Val Gly Ser Ala Pro Ala Ala Ser Leu Gly 260 265 270 Ile Ser Thr Gly Asp Val Ile Thr Ala Val Asp Gly Ala Pro Ile Asn 275 280 285 Ser Ala Thr Ala Met Ala Asp Ala Leu Asn Gly His His Pro Gly Asp 290 295 300 Val Ile Ser Val Thr Trp Gln Thr Lys Ser Gly Gly Thr Arg Thr Gly 305 310 315 320 Asn Val Thr Leu Ala Glu Gly Pro Pro Ala 325 330 7 585 DNA Mycobacterium tuberculosis Ra35 N-terminus of MTB32A (Ra35FL) 7 gccccgccgg ccttgtcgca ggaccggttc gccgacttcc ccgcgctgcc cctcgacccg 60 tccgcgatgg tcgcccaagt ggggccacag gtggtcaaca tcaacaccaa actgggctac 120 aacaacgccg tgggcgccgg gaccggcatc gtcatcgatc ccaacggtgt cgtgctgacc 180 aacaaccacg tgatcgcggg cgccaccgac atcaatgcgt tcagcgtcgg ctccggccaa 240 acctacggcg tcgatgtggt cgggtatgac cgcacccagg atgtcgcggt gctgcagctg 300 cgcggtgccg gtggcctgcc gtcggcggcg atcggtggcg gcgtcgcggt tggtgagccc 360 gtcgtcgcga tgggcaacag cggtgggcag ggcggaacgc cccgtgcggt gcctggcagg 420 gtggtcgcgc tcggccaaac cgtgcaggcg tcggattcgc tgaccggtgc cgaagagaca 480 ttgaacgggt tgatccagtt cgatgccgcg atccagcccg gtgaggcggg cgggcccgtc 540 gtcaacggcc taggacaggt ggtcggtatg aacacggccg cgtcc 585 8 195 PRT Mycobacterium tuberculosis Ra35 N-terminus of MTB32A (Ra35FL) 8 Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe Ala Asp Phe Pro Ala Leu 1 5 10 15 Pro Leu Asp Pro Ser Ala Met Val Ala Gln Val Ala Pro Gln Val Val 20 25 30 Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn Ala Val Gly Ala Gly Thr 35 40 45 Gly Ile Val Ile Asp Pro Asn Gly Val Val Leu Thr Asn Asn His Val 50 55 60 Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe Ser Val Gly Ser Gly Gln 65 70 75 80 Thr Tyr Gly Val Asp Val Val Gly Tyr Asp Arg Thr Gln Asp Val Ala 85 90 95 Val Leu Gln Leu Arg Gly Ala Gly Gly Leu Pro Ser Ala Ala Ile Gly 100 105 110 Gly Gly Val Ala Val Gly Glu Pro Val Val Ala Met Gly Asn Ser Gly 115 120 125 Gly Gln Gly Gly Thr Pro Arg Ala Val Pro Gly Arg Val Val Ala Leu 130 135 140 Gly Gln Thr Val Gln Ala Ser Asp Ser Leu Thr Gly Ala Glu Glu Thr 145 150 155 160 Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala Ile Gln Pro Gly Asp Ser 165 170 175 Gly Gly Pro Val Val Asn Gly Leu Gly Gln Val Val Gly Met Asn Thr 180 185 190 Ala Ala Ser 195 9 447 DNA Mycobacterium tuberculosis Ra12 or MTBRa12 C-terminus of MTB32A (Ra35FL) 9 cggtatgaac acggccgcgt ccgataactt ccagctgtcc cagggtgggc agggattcgc 60 cattccgatc gggcaggcga tggcgatcgc gggccagatc cgatcgggtg gggggtcacc 120 caccgttcat atcgggccta ccgccttcct cggcttgggt gttgtcgaca acaacggcaa 180 cggcgcacga gtccaacgcg tggtcgggag cgctccggcg gcaagtctcg gcatctccac 240 cggcgacgtg atcaccgcgg tcgacggcgc tccgatcaac tcggccaccg cgatggcgga 300 cgcgcttaac gggcatcatc ccggtgacgt catctcggtg aactggcaaa ccaagtcggg 360 cggcacgcgt acagggaacg tgacattggc cgagggaccc ccggcctgat ttcgtcgygg 420 ataccacccg ccggccggcc aattgga 447 10 132 PRT Mycobacterium tuberculosis Ra 12 or MTBRa12 C-terminus of MTB32A (Ra35FL) 10 Thr Ala Ala Ser Asp Asn Phe Gln Leu Ser Gln Gly Gly Gln Gly Phe 1 5 10 15 Ala Ile Pro Ile Gly Gln Ala Met Ala Ile Ala Gly Gln Ile Arg Ser 20 25 30 Gly Gly Gly Ser Pro Thr Val His Ile Gly Pro Thr Ala Phe Leu Gly 35 40 45 Leu Gly Val Val Asp Asn Asn Gly Asn Gly Ala Arg Val Gln Arg Val 50 55 60 Val Gly Ser Ala Pro Ala Ala Ser Leu Gly Ile Ser Thr Gly Asp Val 65 70 75 80 Ile Thr Ala Val Asp Gly Ala Pro Ile Asn Ser Ala Thr Ala Met Ala 85 90 95 Asp Ala Leu Asn Gly His His Pro Gly Asp Val Ile Ser Val Asn Trp 100 105 110 Gln Thr Lys Ser Gly Gly Thr Arg Thr Gly Asn Val Thr Leu Ala Glu 115 120 125 Gly Pro Pro Ala 130 11 851 DNA Mycobacterium tuberculosis MTB39 (TbH9) 11 ctgcagggtg gcgtggatga gcgtcaccgc ggggcaggcc gagctgaccg ccgcccaggt 60 ccgggttgct gcggcggcct acgagacggc gtatgggctg acggtgcccc cgccggtgat 120 cgccgagaac cgtgctgaac tgatgattct gatagcgacc aacctcttgg ggcaaaacac 180 cccggcgatc gcggtcaacg aggccgaata cggcgagatg tgggcccaag acgccgccgc 240 gatgtttggc tacgccgcgg cgacggcgac ggcgacggcg acgttgctgc cgttcgagga 300 ggcgccggag atgaccagcg cgggtgggct cctcgagcag gccgccgcgg tcgaggaggc 360 ctccgacacc gccgcggcga accagttgat gaacaatgtg ccccaggcgc tgaaacagtt 420 ggcccagccc acgcagggca ccacgccttc ttccaagctg ggtggcctgt ggaagacggt 480 ctcgccgcat cggtcgccga tcagcaacat ggtgtcgatg gccaacaacc acatgtcgat 540 gaccaactcg ggtgtgtcga tgaccaacac cttgagctcg atgttgaagg gctttgctcc 600 ggcggcggcc gcccaggccg tgcaaaccgc ggcgcaaaac ggggtccggg cgatgagctc 660 gctgggcagc tcgctgggtt cttcgggtct gggcggtggg gtggccgcca acttgggtcg 720 ggcggcctcg gtacggtatg gtcaccggga tggcggaaaa tatgcanagt ctggtcggcg 780 gaacggtggt ccggcgtaag gtttaccccc gttttctgga tgcggtgaac ttcgtcaacg 840 gaaacagtta c 851 12 263 PRT Mycobacterium tuberculosis MTB39 (TbH9) 12 Val Ala Trp Met Ser Val Thr Ala Gly Gln Ala Glu Leu Thr Ala Ala 1 5 10 15 Gln Val Arg Val Ala Ala Ala Ala Tyr Glu Thr Ala Tyr Gly Leu Thr 20 25 30 Val Pro Pro Pro Val Ile Ala Glu Asn Arg Ala Glu Leu Met Ile Leu 35 40 45 Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr Pro Ala Ile Ala Val Asn 50 55 60 Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln Asp Ala Ala Ala Met Phe 65 70 75 80 Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr Ala Thr Leu Leu Pro Phe 85 90 95 Glu Glu Ala Pro Glu Met Thr Ser Ala Gly Gly Leu Leu Glu Gln Ala 100 105 110 Ala Ala Val Glu Glu Ala Ser Asp Thr Ala Ala Ala Asn Gln Leu Met 115 120 125 Asn Asn Val Pro Gln Ala Leu Lys Gln Leu Ala Gln Pro Thr Gln Gly 130 135 140 Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu Trp Lys Thr Val Ser Pro 145 150 155 160 His Arg Ser Pro Ile Ser Asn Met Val Ser Met Ala Asn Asn His Met 165 170 175 Ser Met Thr Asn Ser Gly Val Ser Met Thr Asn Thr Leu Ser Ser Met 180 185 190 Leu Lys Gly Phe Ala Pro Ala Ala Ala Ala Gln Ala Val Gln Thr Ala 195 200 205 Ala Gln Asn Gly Val Arg Ala Met Ser Ser Leu Gly Ser Ser Leu Gly 210 215 220 Ser Ser Gly Leu Gly Gly Gly Val Ala Ala Asn Leu Gly Arg Ala Ala 225 230 235 240 Ser Val Arg Tyr Gly His Arg Asp Gly Gly Lys Tyr Ala Xaa Ser Gly 245 250 255 Arg Arg Asn Gly Gly Pro Ala 260 13 3058 DNA Mycobacterium tuberculosis MTB39 (TbH9FL) 13 gatcgtaccc gtgcgagtgc tcgggccgtt tgaggatgga gtgcacgtgt ctttcgtgat 60 ggcataccca gagatgttgg cggcggcggc tgacaccctg cagagcatcg gtgctaccac 120 tgtggctagc aatgccgctg cggcggcccc gacgactggg gtggtgcccc ccgctgccga 180 tgaggtgtcg gcgctgactg cggcgcactt cgccgcacat gcggcgatgt atcagtccgt 240 gagcgctcgg gctgctgcga ttcatgacca gttcgtggcc acccttgcca gcagcgccag 300 ctcgtatgcg gccactgaag tcgccaatgc ggcggcggcc agctaagcca ggaacagtcg 360 gcacgagaaa ccacgagaaa tagggacacg taatggtgga tttcggggcg ttaccaccgg 420 agatcaactc cgcgaggatg tacgccggcc cgggttcggc ctcgctggtg gccgcggctc 480 agatgtggga cagcgtggcg agtgacctgt tttcggccgc gtcggcgttt cagtcggtgg 540 tctggggtct gacggtgggg tcgtggatag gttcgtcggc gggtctgatg gtggcggcgg 600 cctcgccgta tgtggcgtgg atgagcgtca ccgcggggca ggccgagctg accgccgccc 660 aggtccgggt tgctgcggcg gcctacgaga cggcgtatgg gctgacggtg cccccgccgg 720 tgatcgccga gaaccgtgct gaactgatga ttctgatagc gaccaacctc ttggggcaaa 780 acaccccggc gatcgcggtc aacgaggccg aatacggcga gatgtgggcc caagacgccg 840 ccgcgatgtt tggctacgcc gcggcgacgg cgacggcgac ggcgacgttg ctgccgttcg 900 aggaggcgcc ggagatgacc agcgcgggtg ggctcctcga gcaggccgcc gcggtcgagg 960 aggcctccga caccgccgcg gcgaaccagt tgatgaacaa tgtgccccag gcgctgcaac 1020 agctggccca gcccacgcag ggcaccacgc cttcttccaa gctgggtggc ctgtggaaga 1080 cggtctcgcc gcatcggtcg ccgatcagca acatggtgtc gatggccaac aaccacatgt 1140 cgatgaccaa ctcgggtgtg tcgatgacca acaccttgag ctcgatgttg aagggctttg 1200 ctccggcggc ggccgcccag gccgtgcaaa ccgcggcgca aaacggggtc cgggcgatga 1260 gctcgctggg cagctcgctg ggttcttcgg gtctgggcgg tggggtggcc gccaacttgg 1320 gtcgggcggc ctcggtcggt tcgttgtcgg tgccgcaggc ctgggccgcg gccaaccagg 1380 cagtcacccc ggcggcgcgg gcgctgccgc tgaccagcct gaccagcgcc gcggaaagag 1440 ggcccgggca gatgctgggc gggctgccgg tggggcagat gggcgccagg gccggtggtg 1500 ggctcagtgg tgtgctgcgt gttccgccgc gaccctatgt gatgccgcat tctccggcgg 1560 ccggctagga gagggggcgc agactgtcgt tatttgacca gtgatcggcg gtctcggtgt 1620 ttccgcggcc ggctatgaca acagtcaatg tgcatgacaa gttacaggta ttaggtccag 1680 gttcaacaag gagacaggca acatggcctc acgttttatg acggatccgc acgcgatgcg 1740 ggacatggcg ggccgttttg aggtgcacgc ccagacggtg gaggacgagg ctcgccggat 1800 gtgggcgtcc gcgcaaaaca tttccggtgc gggctggagt ggcatggccg aggcgacctc 1860 gctagacacc atggcccaga tgaatcaggc gtttcgcaac atcgtgaaca tgctgcacgg 1920 ggtgcgtgac gggctggttc gcgacgccaa caactacgag cagcaagagc aggcctccca 1980 gcagatcctc agcagctaac gtcagccgct gcagcacaat acttttacaa gcgaaggaga 2040 acaggttcga tgaccatcaa ctatcaattc ggggatgtcg acgctcacgg cgccatgatc 2100 cgcgctcagg ccgggttgct ggaggccgag catcaggcca tcattcgtga tgtgttgacc 2160 gcgagtgact tttggggcgg cgccggttcg gcggcctgcc aggggttcat tacccagttg 2220 ggccgtaact tccaggtgat ctacgagcag gccaacgccc acgggcagaa ggtgcaggct 2280 gccggcaaca acatggcgca aaccgacagc gccgtcggct ccagctgggc ctgacaccag 2340 gccaaggcca gggacgtggt gtacgagtga agttcctcgc gtgatccttc gggtggcagt 2400 ctaagtggtc agtgctgggg tgttggtggt ttgctgcttg gcgggttctt cggtgctggt 2460 cagtgctgct cgggctcggg tgaggacctc gaggcccagg tagcgccgtc cttcgatcca 2520 ttcgtcgtgt tgttcggcga ggacggctcc gacgaggcgg atgatcgagg cgcggtcggg 2580 gaagatgccc acgacgtcgg ttcggcgtcg tacctctcgg ttgaggcgtt cctgggggtt 2640 gttggaccag atttggcgcc agatctgctt ggggaaggcg gtgaacgcca gcaggtcggt 2700 gcgggcggtg tcgaggtgct cggccaccgc ggggagtttg tcggtcagag cgtcgagtac 2760 ccgatcatat tgggcaacaa ctgattcggc gtcgggctgg tcgtagatgg agtgcagcag 2820 ggtgcgcacc cacggccagg agggcttcgg ggtggctgcc atcagattgg ctgcgtagtg 2880 ggttctgcag cgctgccagg ccgctgcggg cagggtggcg ccgatcgcgg ccaccaggcc 2940 ggcgtgggcg tcgctggtga ccagcgcgac cccggacagg ccgcgggcga ccaggtcgcg 3000 gaagaacgcc agccagccgg ccccgtcctc ggcggaggtg acctggatgc ccaggatc 3058 14 391 PRT Mycobacterium tuberculosis MTB39 (TbH9FL) 14 Met Val Asp Phe Gly Ala Leu Pro Pro Glu Ile Asn Ser Ala Arg Met 1 5 10 15 Tyr Ala Gly Pro Gly Ser Ala Ser Leu Val Ala Ala Ala Gln Met Trp 20 25 30 Asp Ser Val Ala Ser Asp Leu Phe Ser Ala Ala Ser Ala Phe Gln Ser 35 40 45 Val Val Trp Gly Leu Thr Val Gly Ser Trp Ile Gly Ser Ser Ala Gly 50 55 60 Leu Met Val Ala Ala Ala Ser Pro Tyr Val Ala Trp Met Ser Val Thr 65 70 75 80 Ala Gly Gln Ala Glu Leu Thr Ala Ala Gln Val Arg Val Ala Ala Ala 85 90 95 Ala Tyr Glu Thr Ala Tyr Gly Leu Thr Val Pro Pro Pro Val Ile Ala 100 105 110 Glu Asn Arg Ala Glu Leu Met Ile Leu Ile Ala Thr Asn Leu Leu Gly 115 120 125 Gln Asn Thr Pro Ala Ile Ala Val Asn Glu Ala Glu Tyr Gly Glu Met 130 135 140 Trp Ala Gln Asp Ala Ala Ala Met Phe Gly Tyr Ala Ala Ala Thr Ala 145 150 155 160 Thr Ala Thr Ala Thr Leu Leu Pro Phe Glu Glu Ala Pro Glu Met Thr 165 170 175 Ser Ala Gly Gly Leu Leu Glu Gln Ala Ala Ala Val Glu Glu Ala Ser 180 185 190 Asp Thr Ala Ala Ala Asn Gln Leu Met Asn Asn Val Pro Gln Ala Leu 195 200 205 Gln Gln Leu Ala Gln Pro Thr Gln Gly Thr Thr Pro Ser Ser Lys Leu 210 215 220 Gly Gly Leu Trp Lys Thr Val Ser Pro His Arg Ser Pro Ile Ser Asn 225 230 235 240 Met Val Ser Met Ala Asn Asn His Met Ser Met Thr Asn Ser Gly Val 245 250 255 Ser Met Thr Asn Thr Leu Ser Ser Met Leu Lys Gly Phe Ala Pro Ala 260 265 270 Ala Ala Ala Gln Ala Val Gln Thr Ala Ala Gln Asn Gly Val Arg Ala 275 280 285 Met Ser Ser Leu Gly Ser Ser Leu Gly Ser Ser Gly Leu Gly Gly Gly 290 295 300 Val Ala Ala Asn Leu Gly Arg Ala Ala Ser Val Gly Ser Leu Ser Val 305 310 315 320 Pro Gln Ala Trp Ala Ala Ala Asn Gln Ala Val Thr Pro Ala Ala Arg 325 330 335 Ala Leu Pro Leu Thr Ser Leu Thr Ser Ala Ala Glu Arg Gly Pro Gly 340 345 350 Gln Met Leu Gly Gly Leu Pro Val Gly Gln Met Gly Ala Arg Ala Gly 355 360 365 Gly Gly Leu Ser Gly Val Leu Arg Val Pro Pro Arg Pro Tyr Val Met 370 375 380 Pro His Ser Pro Ala Ala Gly 385 390 15 2287 DNA Artificial Sequence Description of Artificial Sequencetri-fusion protein MTB72F (Ra12-TbH9-Ra35 or MTB32-MTB39 fusion) 15 tctagaaata attttgttta ctttaagaan ganatataca t atg cat cac cat cac 56 Met His His His His 1 5 cat cac acg gcc gcg tcc gat aac ttc cag ctg tcc cag ggt ggg cag 104 His His Thr Ala Ala Ser Asp Asn Phe Gln Leu Ser Gln Gly Gly Gln 10 15 20 gga ttc gcc att ccg atc ggg cag gcg atg gcg atc gcg ggc cag atc 152 Gly Phe Ala Ile Pro Ile Gly Gln Ala Met Ala Ile Ala Gly Gln Ile 25 30 35 cga tcg ggt ggg ggg tca ccc acc gtt cat atc ggg cct acc gcc ttc 200 Arg Ser Gly Gly Gly Ser Pro Thr Val His Ile Gly Pro Thr Ala Phe 40 45 50 ctc ggc ttg ggt gtt gtc gac aac aac ggc aac ggc gca cga gtc caa 248 Leu Gly Leu Gly Val Val Asp Asn Asn Gly Asn Gly Ala Arg Val Gln 55 60 65 cgc gtg gtc ggg agc gct ccg gcg gca agt ctc ggc atc tcc acc ggc 296 Arg Val Val Gly Ser Ala Pro Ala Ala Ser Leu Gly Ile Ser Thr Gly 70 75 80 85 gac gtg atc acc gcg gtc gac ggc gct ccg atc aac tcg gcc acc gcg 344 Asp Val Ile Thr Ala Val Asp Gly Ala Pro Ile Asn Ser Ala Thr Ala 90 95 100 atg gcg gac gcg ctt aac ggg cat cat ccc ggt gac gtc atc tcg gtg 392 Met Ala Asp Ala Leu Asn Gly His His Pro Gly Asp Val Ile Ser Val 105 110 115 acc tgg caa acc aag tcg ggc ggc acg cgt aca ggg aac gtg aca ttg 440 Thr Trp Gln Thr Lys Ser Gly Gly Thr Arg Thr Gly Asn Val Thr Leu 120 125 130 gcc gag gga ccc ccg gcc gaa ttc atg gtg gat ttc ggg gcg tta cca 488 Ala Glu Gly Pro Pro Ala Glu Phe Met Val Asp Phe Gly Ala Leu Pro 135 140 145 ccg gag atc aac tcc gcg agg atg tac gcc ggc ccg ggt tcg gcc tcg 536 Pro Glu Ile Asn Ser Ala Arg Met Tyr Ala Gly Pro Gly Ser Ala Ser 150 155 160 165 ctg gtg gcc gcg gct cag atg tgg gac agc gtg gcg agt gac ctg ttt 584 Leu Val Ala Ala Ala Gln Met Trp Asp Ser Val Ala Ser Asp Leu Phe 170 175 180 tcg gcc gcg tcg gcg ttt cag tcg gtg gtc tgg ggt ctg acg gtg ggg 632 Ser Ala Ala Ser Ala Phe Gln Ser Val Val Trp Gly Leu Thr Val Gly 185 190 195 tcg tgg ata ggt tcg tcg gcg ggt ctg atg gtg gcg gcg gcc tcg ccg 680 Ser Trp Ile Gly Ser Ser Ala Gly Leu Met Val Ala Ala Ala Ser Pro 200 205 210 tat gtg gcg tgg atg agc gtc acc gcg ggg cag gcc gag ctg acc gcc 728 Tyr Val Ala Trp Met Ser Val Thr Ala Gly Gln Ala Glu Leu Thr Ala 215 220 225 gcc cag gtc cgg gtt gct gcg gcg gcc tac gag acg gcg tat ggg ctg 776 Ala Gln Val Arg Val Ala Ala Ala Ala Tyr Glu Thr Ala Tyr Gly Leu 230 235 240 245 acg gtg ccc ccg ccg gtg atc gcc gag aac cgt gct gaa ctg atg att 824 Thr Val Pro Pro Pro Val Ile Ala Glu Asn Arg Ala Glu Leu Met Ile 250 255 260 ctg ata gcg acc aac ctc ttg ggg caa aac acc ccg gcg atc gcg gtc 872 Leu Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr Pro Ala Ile Ala Val 265 270 275 aac gag gcc gaa tac ggc gag atg tgg gcc caa gac gcc gcc gcg atg 920 Asn Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln Asp Ala Ala Ala Met 280 285 290 ttt ggc tac gcc gcg gcg acg gcg acg gcg acg gcg acg ttg ctg ccg 968 Phe Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr Ala Thr Leu Leu Pro 295 300 305 ttc gag gag gcg ccg gag atg acc agc gcg ggt ggg ctc ctc gag cag 1016 Phe Glu Glu Ala Pro Glu Met Thr Ser Ala Gly Gly Leu Leu Glu Gln 310 315 320 325 gcc gcc gcg gtc gag gag gcc tcc gac acc gcc gcg gcg aac cag ttg 1064 Ala Ala Ala Val Glu Glu Ala Ser Asp Thr Ala Ala Ala Asn Gln Leu 330 335 340 atg aac aat gtg ccc cag gcg ctg caa cag ctg gcc cag ccc acg cag 1112 Met Asn Asn Val Pro Gln Ala Leu Gln Gln Leu Ala Gln Pro Thr Gln 345 350 355 ggc acc acg cct tct tcc aag ctg ggt ggc ctg tgg aag acg gtc tcg 1160 Gly Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu Trp Lys Thr Val Ser 360 365 370 ccg cat cgg tcg ccg atc agc aac atg gtg tcg atg gcc aac aac cac 1208 Pro His Arg Ser Pro Ile Ser Asn Met Val Ser Met Ala Asn Asn His 375 380 385 atg tcg atg acc aac tcg ggt gtg tcg atg acc aac acc ttg agc tcg 1256 Met Ser Met Thr Asn Ser Gly Val Ser Met Thr Asn Thr Leu Ser Ser 390 395 400 405 atg ttg aag ggc ttt gct ccg gcg gcg gcc cgc cag gcc gtg caa acc 1304 Met Leu Lys Gly Phe Ala Pro Ala Ala Ala Arg Gln Ala Val Gln Thr 410 415 420 gcg gcg caa aac ggg gtc cgg gcg atg agc tcg ctg ggc agc tcg ctg 1352 Ala Ala Gln Asn Gly Val Arg Ala Met Ser Ser Leu Gly Ser Ser Leu 425 430 435 ggt tct tcg ggt ctg ggc ggt ggg gtg gcc gcc aac ttg ggt cgg gcg 1400 Gly Ser Ser Gly Leu Gly Gly Gly Val Ala Ala Asn Leu Gly Arg Ala 440 445 450 gcc tcg gtc ggt tcg ttg tcg gtg ccg cag gcc tgg gcc gcg gcc aac 1448 Ala Ser Val Gly Ser Leu Ser Val Pro Gln Ala Trp Ala Ala Ala Asn 455 460 465 cag gca gtc acc ccg gcg gcg cgg gcg ctg ccg ctg acc agc ctg acc 1496 Gln Ala Val Thr Pro Ala Ala Arg Ala Leu Pro Leu Thr Ser Leu Thr 470 475 480 485 agc gcc gcg gaa aga ggg ccc ggg cag atg ctg ggc ggg ctg ccg gtg 1544 Ser Ala Ala Glu Arg Gly Pro Gly Gln Met Leu Gly Gly Leu Pro Val 490 495 500 ggg cag atg ggc gcc agg gcc ggt ggt ggg ctc agt ggt gtg ctg cgt 1592 Gly Gln Met Gly Ala Arg Ala Gly Gly Gly Leu Ser Gly Val Leu Arg 505 510 515 gtt ccg ccg cga ccc tat gtg atg ccg cat tct ccg gca gcc ggc gat 1640 Val Pro Pro Arg Pro Tyr Val Met Pro His Ser Pro Ala Ala Gly Asp 520 525 530 atc gcc ccg ccg gcc ttg tcg cag gac cgg ttc gcc gac ttc ccc gcg 1688 Ile Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe Ala Asp Phe Pro Ala 535 540 545 ctg ccc ctc gac ccg tcc gcg atg gtc gcc caa gtg ggg cca cag gtg 1736 Leu Pro Leu Asp Pro Ser Ala Met Val Ala Gln Val Gly Pro Gln Val 550 555 560 565 gtc aac atc aac acc aaa ctg ggc tac aac aac gcc gtg ggc gcc ggg 1784 Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn Ala Val Gly Ala Gly 570 575 580 acc ggc atc gtc atc gat ccc aac ggt gtc gtg ctg acc aac aac cac 1832 Thr Gly Ile Val Ile Asp Pro Asn Gly Val Val Leu Thr Asn Asn His 585 590 595 gtg atc gcg ggc gcc acc gac atc aat gcg ttc agc gtc ggc tcc ggc 1880 Val Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe Ser Val Gly Ser Gly 600 605 610 caa acc tac ggc gtc gat gtg gtc ggg tat gac cgc acc cag gat gtc 1928 Gln Thr Tyr Gly Val Asp Val Val Gly Tyr Asp Arg Thr Gln Asp Val 615 620 625 gcg gtg ctg cag ctg cgc ggt gcc ggt ggc ctg ccg tcg gcg gcg atc 1976 Ala Val Leu Gln Leu Arg Gly Ala Gly Gly Leu Pro Ser Ala Ala Ile 630 635 640 645 ggt ggc ggc gtc gcg gtt ggt gag ccc gtc gtc gcg atg ggc aac agc 2024 Gly Gly Gly Val Ala Val Gly Glu Pro Val Val Ala Met Gly Asn Ser 650 655 660 ggt ggg cag ggc gga acg ccc cgt gcg gtg cct ggc agg gtg gtc gcg 2072 Gly Gly Gln Gly Gly Thr Pro Arg Ala Val Pro Gly Arg Val Val Ala 665 670 675 ctc ggc caa acc gtg cag gcg tcg gat tcg ctg acc ggt gcc gaa gag 2120 Leu Gly Gln Thr Val Gln Ala Ser Asp Ser Leu Thr Gly Ala Glu Glu 680 685 690 aca ttg aac ggg ttg atc cag ttc gat gcc gcg atc cag ccc ggt gat 2168 Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala Ile Gln Pro Gly Asp 695 700 705 tcg ggc ggg ccc gtc gtc aac ggc cta gga cag gtg gtc ggt atg aac 2216 Ser Gly Gly Pro Val Val Asn Gly Leu Gly Gln Val Val Gly Met Asn 710 715 720 725 acg gcc gcg tcc tag gatatccatc acactggcgg ccgctcgagc agatccggnt 2271 Thr Ala Ala Ser gtaacaaagc ccgaaa 2287 16 729 PRT Artificial Sequence Description of Artificial Sequencetri-fusion protein MTB72F (Ra12-TbH9-Ra35 or MTB32-MTB39 fusion) 16 Met His His His His His His Thr Ala Ala Ser Asp Asn Phe Gln Leu 1 5 10 15 Ser Gln Gly Gly Gln Gly Phe Ala Ile Pro Ile Gly Gln Ala Met Ala 20 25 30 Ile Ala Gly Gln Ile Arg Ser Gly Gly Gly Ser Pro Thr Val His Ile 35 40 45 Gly Pro Thr Ala Phe Leu Gly Leu Gly Val Val Asp Asn Asn Gly Asn 50 55 60 Gly Ala Arg Val Gln Arg Val Val Gly Ser Ala Pro Ala Ala Ser Leu 65 70 75 80 Gly Ile Ser Thr Gly Asp Val Ile Thr Ala Val Asp Gly Ala Pro Ile 85 90 95 Asn Ser Ala Thr Ala Met Ala Asp Ala Leu Asn Gly His His Pro Gly 100 105 110 Asp Val Ile Ser Val Thr Trp Gln Thr Lys Ser Gly Gly Thr Arg Thr 115 120 125 Gly Asn Val Thr Leu Ala Glu Gly Pro Pro Ala Glu Phe Met Val Asp 130 135 140 Phe Gly Ala Leu Pro Pro Glu Ile Asn Ser Ala Arg Met Tyr Ala Gly 145 150 155 160 Pro Gly Ser Ala Ser Leu Val Ala Ala Ala Gln Met Trp Asp Ser Val 165 170 175 Ala Ser Asp Leu Phe Ser Ala Ala Ser Ala Phe Gln Ser Val Val Trp 180 185 190 Gly Leu Thr Val Gly Ser Trp Ile Gly Ser Ser Ala Gly Leu Met Val 195 200 205 Ala Ala Ala Ser Pro Tyr Val Ala Trp Met Ser Val Thr Ala Gly Gln 210 215 220 Ala Glu Leu Thr Ala Ala Gln Val Arg Val Ala Ala Ala Ala Tyr Glu 225 230 235 240 Thr Ala Tyr Gly Leu Thr Val Pro Pro Pro Val Ile Ala Glu Asn Arg 245 250 255 Ala Glu Leu Met Ile Leu Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr 260 265 270 Pro Ala Ile Ala Val Asn Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln 275 280 285 Asp Ala Ala Ala Met Phe Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr 290 295 300 Ala Thr Leu Leu Pro Phe Glu Glu Ala Pro Glu Met Thr Ser Ala Gly 305 310 315 320 Gly Leu Leu Glu Gln Ala Ala Ala Val Glu Glu Ala Ser Asp Thr Ala 325 330 335 Ala Ala Asn Gln Leu Met Asn Asn Val Pro Gln Ala Leu Gln Gln Leu 340 345 350 Ala Gln Pro Thr Gln Gly Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu 355 360 365 Trp Lys Thr Val Ser Pro His Arg Ser Pro Ile Ser Asn Met Val Ser 370 375 380 Met Ala Asn Asn His Met Ser Met Thr Asn Ser Gly Val Ser Met Thr 385 390 395 400 Asn Thr Leu Ser Ser Met Leu Lys Gly Phe Ala Pro Ala Ala Ala Arg 405 410 415 Gln Ala Val Gln Thr Ala Ala Gln Asn Gly Val Arg Ala Met Ser Ser 420 425 430 Leu Gly Ser Ser Leu Gly Ser Ser Gly Leu Gly Gly Gly Val Ala Ala 435 440 445 Asn Leu Gly Arg Ala Ala Ser Val Gly Ser Leu Ser Val Pro Gln Ala 450 455 460 Trp Ala Ala Ala Asn Gln Ala Val Thr Pro Ala Ala Arg Ala Leu Pro 465 470 475 480 Leu Thr Ser Leu Thr Ser Ala Ala Glu Arg Gly Pro Gly Gln Met Leu 485 490 495 Gly Gly Leu Pro Val Gly Gln Met Gly Ala Arg Ala Gly Gly Gly Leu 500 505 510 Ser Gly Val Leu Arg Val Pro Pro Arg Pro Tyr Val Met Pro His Ser 515 520 525 Pro Ala Ala Gly Asp Ile Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe 530 535 540 Ala Asp Phe Pro Ala Leu Pro Leu Asp Pro Ser Ala Met Val Ala Gln 545 550 555 560 Val Gly Pro Gln Val Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn 565 570 575 Ala Val Gly Ala Gly Thr Gly Ile Val Ile Asp Pro Asn Gly Val Val 580 585 590 Leu Thr Asn Asn His Val Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe 595 600 605 Ser Val Gly Ser Gly Gln Thr Tyr Gly Val Asp Val Val Gly Tyr Asp 610 615 620 Arg Thr Gln Asp Val Ala Val Leu Gln Leu Arg Gly Ala Gly Gly Leu 625 630 635 640 Pro Ser Ala Ala Ile Gly Gly Gly Val Ala Val Gly Glu Pro Val Val 645 650 655 Ala Met Gly Asn Ser Gly Gly Gln Gly Gly Thr Pro Arg Ala Val Pro 660 665 670 Gly Arg Val Val Ala Leu Gly Gln Thr Val Gln Ala Ser Asp Ser Leu 675 680 685 Thr Gly Ala Glu Glu Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala 690 695 700 Ile Gln Pro Gly Asp Ser Gly Gly Pro Val Val Asn Gly Leu Gly Gln 705 710 715 720 Val Val Gly Met Asn Thr Ala Ala Ser 725 17 2190 DNA Artificial Sequence Description of Artificial SequenceMTB72FMutSA (Ra12-TbHp-Ra35MutSA) cDNA 17 atgcatcacc atcaccatca cacggccgcg tccgataact tccagctgtc ccagggtggg 60 cagggattcg ccattccgat cgggcaggcg atggcgatcg cgggccagat ccgatcgggt 120 ggggggtcac ccaccgttca tatcgggcct accgccttcc tcggcttggg tgttgtcgac 180 aacaacggca acggcgcacg agtccaacgc gtggtcggga gcgctccggc ggcaagtctc 240 ggcatctcca ccggcgacgt gatcaccgcg gtcgacggcg ctccgatcaa ctcggccacc 300 gcgatggcgg acgcgcttaa cgggcatcat cccggtgacg tcatctcggt gacctggcaa 360 accaagtcgg gcggcacgcg tacagggaac gtgacattgg ccgagggacc cccggccgaa 420 ttcatggtgg atttcggggc gttaccaccg gagatcaact ccgcgaggat gtacgccggc 480 ccgggttcgg cctcgctggt ggccgcggct cagatgtggg acagcgtggc gagtgacctg 540 ttttcggccg cgtcggcgtt tcagtcggtg gtctggggtc tgacggtggg gtcgtggata 600 ggttcgtcgg cgggtctgat ggtggcggcg gcctcgccgt atgtggcgtg gatgagcgtc 660 accgcggggc aggccgagct gaccgccgcc caggtccggg ttgctgcggc ggcctacgag 720 acggcgtatg ggctgacggt gcccccgccg gtgatcgccg agaaccgtgc tgaactgatg 780 attctgatag cgaccaacct cttggggcaa aacaccccgg cgatcgcggt caacgaggcc 840 gaatacggcg agatgtgggc ccaagacgcc gccgcgatgt ttggctacgc cgcggcgacg 900 gcgacggcga cggcgacgtt gctgccgttc gaggaggcgc cggagatgac cagcgcgggt 960 gggctcctcg agcaggccgc cgcggtcgag gaggcctccg acaccgccgc ggcgaaccag 1020 ttgatgaaca atgtgcccca ggcgctgcaa cagctggccc agcccacgca gggcaccacg 1080 ccttcttcca agctgggtgg cctgtggaag acggtctcgc cgcatcggtc gccgatcagc 1140 aacatggtgt cgatggccaa caaccacatg tcgatgacca actcgggtgt gtcgatgacc 1200 aacaccttga gctcgatgtt gaagggcttt gctccggcgg cggccgccca ggccgtgcaa 1260 accgcggcgc aaaacggggt ccgggcgatg agctcgctgg gcagctcgct gggttcttcg 1320 ggtctgggcg gtggggtggc cgccaacttg ggtcgggcgg cctcggtcgg ttcgttgtcg 1380 gtgccgcagg cctgggccgc ggccaaccag gcagtcaccc cggcggcgcg ggcgctgccg 1440 ctgaccagcc tgaccagcgc cgcggaaaga gggcccgggc agatgctggg cgggctgccg 1500 gtggggcaga tgggcgccag ggccggtggt gggctcagtg gtgtgctgcg tgttccgccg 1560 cgaccctatg tgatgccgca ttctccggca gccggcgata tcgccccgcc ggccttgtcg 1620 caggaccggt tcgccgactt ccccgcgctg cccctcgacc cgtccgcgat ggtcgcccaa 1680 gtggggccac aggtggtcaa catcaacacc aaactgggct acaacaacgc cgtgggcgcc 1740 gggaccggca tcgtcatcga tcccaacggt gtcgtgctga ccaacaacca cgtgatcgcg 1800 ggcgccaccg acatcaatgc gttcagcgtc ggctccggcc aaacctacgg cgtcgatgtg 1860 gtcgggtatg accgcaccca ggatgtcgcg gtgctgcagc tgcgcggtgc cggtggcctg 1920 ccgtcggcgg cgatcggtgg cggcgtcgcg gttggtgagc ccgtcgtcgc gatgggcaac 1980 agcggtgggc agggcggaac gccccgtgcg gtgcctggca gggtggtcgc gctcggccaa 2040 accgtgcagg cgtcggattc gctgaccggt gccgaagaga cattgaacgg gttgatccag 2100 ttcgatgccg cgatccagcc cggtgatgcg ggcgggcccg tcgtcaacgg cctaggacag 2160 gtggtcggta tgaacacggc cgcgtcctag 2190 18 729 PRT Artificial Sequence Description of Artificial SequenceMTB72FMutSA (Ra12-TbHp-Ra35MutSA) 18 Met His His His His His His Thr Ala Ala Ser Asp Asn Phe Gln Leu 1 5 10 15 Ser Gln Gly Gly Gln Gly Phe Ala Ile Pro Ile Gly Gln Ala Met Ala 20 25 30 Ile Ala Gly Gln Ile Arg Ser Gly Gly Gly Ser Pro Thr Val His Ile 35 40 45 Gly Pro Thr Ala Phe Leu Gly Leu Gly Val Val Asp Asn Asn Gly Asn 50 55 60 Gly Ala Arg Val Gln Arg Val Val Gly Ser Ala Pro Ala Ala Ser Leu 65 70 75 80 Gly Ile Ser Thr Gly Asp Val Ile Thr Ala Val Asp Gly Ala Pro Ile 85 90 95 Asn Ser Ala Thr Ala Met Ala Asp Ala Leu Asn Gly His His Pro Gly 100 105 110 Asp Val Ile Ser Val Thr Trp Gln Thr Lys Ser Gly Gly Thr Arg Thr 115 120 125 Gly Asn Val Thr Leu Ala Glu Gly Pro Pro Ala Glu Phe Met Val Asp 130 135 140 Phe Gly Ala Leu Pro Pro Glu Ile Asn Ser Ala Arg Met Tyr Ala Gly 145 150 155 160 Pro Gly Ser Ala Ser Leu Val Ala Ala Ala Gln Met Trp Asp Ser Val 165 170 175 Ala Ser Asp Leu Phe Ser Ala Ala Ser Ala Phe Gln Ser Val Val Trp 180 185 190 Gly Leu Thr Val Gly Ser Trp Ile Gly Ser Ser Ala Gly Leu Met Val 195 200 205 Ala Ala Ala Ser Pro Tyr Val Ala Trp Met Ser Val Thr Ala Gly Gln 210 215 220 Ala Glu Leu Thr Ala Ala Gln Val Arg Val Ala Ala Ala Ala Tyr Glu 225 230 235 240 Thr Ala Tyr Gly Leu Thr Val Pro Pro Pro Val Ile Ala Glu Asn Arg 245 250 255 Ala Glu Leu Met Ile Leu Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr 260 265 270 Pro Ala Ile Ala Val Asn Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln 275 280 285 Asp Ala Ala Ala Met Phe Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr 290 295 300 Ala Thr Leu Leu Pro Phe Glu Glu Ala Pro Glu Met Thr Ser Ala Gly 305 310 315 320 Gly Leu Leu Glu Gln Ala Ala Ala Val Glu Glu Ala Ser Asp Thr Ala 325 330 335 Ala Ala Asn Gln Leu Met Asn Asn Val Pro Gln Ala Leu Gln Gln Leu 340 345 350 Ala Gln Pro Thr Gln Gly Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu 355 360 365 Trp Lys Thr Val Ser Pro His Arg Ser Pro Ile Ser Asn Met Val Ser 370 375 380 Met Ala Asn Asn His Met Ser Met Thr Asn Ser Gly Val Ser Met Thr 385 390 395 400 Asn Thr Leu Ser Ser Met Leu Lys Gly Phe Ala Pro Ala Ala Ala Ala 405 410 415 Gln Ala Val Gln Thr Ala Ala Gln Asn Gly Val Arg Ala Met Ser Ser 420 425 430 Leu Gly Ser Ser Leu Gly Ser Ser Gly Leu Gly Gly Gly Val Ala Ala 435 440 445 Asn Leu Gly Arg Ala Ala Ser Val Gly Ser Leu Ser Val Pro Gln Ala 450 455 460 Trp Ala Ala Ala Asn Gln Ala Val Thr Pro Ala Ala Arg Ala Leu Pro 465 470 475 480 Leu Thr Ser Leu Thr Ser Ala Ala Glu Arg Gly Pro Gly Gln Met Leu 485 490 495 Gly Gly Leu Pro Val Gly Gln Met Gly Ala Arg Ala Gly Gly Gly Leu 500 505 510 Ser Gly Val Leu Arg Val Pro Pro Arg Pro Tyr Val Met Pro His Ser 515 520 525 Pro Ala Ala Gly Asp Ile Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe 530 535 540 Ala Asp Phe Pro Ala Leu Pro Leu Asp Pro Ser Ala Met Val Ala Gln 545 550 555 560 Val Gly Pro Gln Val Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn 565 570 575 Ala Val Gly Ala Gly Thr Gly Ile Val Ile Asp Pro Asn Gly Val Val 580 585 590 Leu Thr Asn Asn His Val Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe 595 600 605 Ser Val Gly Ser Gly Gln Thr Tyr Gly Val Asp Val Val Gly Tyr Asp 610 615 620 Arg Thr Gln Asp Val Ala Val Leu Gln Leu Arg Gly Ala Gly Gly Leu 625 630 635 640 Pro Ser Ala Ala Ile Gly Gly Gly Val Ala Val Gly Glu Pro Val Val 645 650 655 Ala Met Gly Asn Ser Gly Gly Gln Gly Gly Thr Pro Arg Ala Val Pro 660 665 670 Gly Arg Val Val Ala Leu Gly Gln Thr Val Gln Ala Ser Asp Ser Leu 675 680 685 Thr Gly Ala Glu Glu Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala 690 695 700 Ile Gln Pro Gly Asp Ala Gly Gly Pro Val Val Asn Gly Leu Gly Gln 705 710 715 720 Val Val Gly Met Asn Thr Ala Ala Ser 725 19 1797 DNA Artificial Sequence Description of Artificial Sequencebi-fusion protein TbH9-Ra35 (designated MTB59F) 19 cat atg cat cac cat cac cat cac atg gtg gat ttc ggg gcg tta cca 48 His Met His His His His His His Met Val Asp Phe Gly Ala Leu Pro 1 5 10 15 ccg gag atc aac tcc gcg agg atg tac gcc ggc ccg ggt tcg gcc tcg 96 Pro Glu Ile Asn Ser Ala Arg Met Tyr Ala Gly Pro Gly Ser Ala Ser 20 25 30 ctg gtg gcc gcg gct cag atg tgg gac agc gtg gcg agt gac ctg ttt 144 Leu Val Ala Ala Ala Gln Met Trp Asp Ser Val Ala Ser Asp Leu Phe 35 40 45 tcg gcc gcg tcg gcg ttt cag tcg gtg gtc tgg ggt ctg acg gtg ggg 192 Ser Ala Ala Ser Ala Phe Gln Ser Val Val Trp Gly Leu Thr Val Gly 50 55 60 tcg tgg ata ggt tcg tcg gcg ggt ctg atg gtg gcg gcg gcc tcg ccg 240 Ser Trp Ile Gly Ser Ser Ala Gly Leu Met Val Ala Ala Ala Ser Pro 65 70 75 80 tat gtg gcg tgg atg agc gtc acc gcg ggg cag gcc gag ctg acc gcc 288 Tyr Val Ala Trp Met Ser Val Thr Ala Gly Gln Ala Glu Leu Thr Ala 85 90 95 gcc cag gtc cgg gtt gct gcg gcg gcc tac gag acg gcg tat ggg ctg 336 Ala Gln Val Arg Val Ala Ala Ala Ala Tyr Glu Thr Ala Tyr Gly Leu 100 105 110 acg gtg ccc ccg ccg gtg atc gcc gag aac cgt gct gaa ctg atg att 384 Thr Val Pro Pro Pro Val Ile Ala Glu Asn Arg Ala Glu Leu Met Ile 115 120 125 ctg ata gcg acc aac ctc ttg ggg caa aac acc ccg gcg atc gcg gtc 432 Leu Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr Pro Ala Ile Ala Val 130 135 140 aac gag gcc gaa tac ggc gag atg tgg gcc caa gac gcc gcc gcg atg 480 Asn Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln Asp Ala Ala Ala Met 145 150 155 160 ttt ggc tac gcc gcg gcg acg gcg acg gcg acg gcg acg ttg ctg ccg 528 Phe Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr Ala Thr Leu Leu Pro 165 170 175 ttc gag gag gcg ccg gag atg acc agc gcg ggt ggg ctc ctc gag cag 576 Phe Glu Glu Ala Pro Glu Met Thr Ser Ala Gly Gly Leu Leu Glu Gln 180 185 190 gcc gcc gcg gtc gag gag gcc tcc gac acc gcc gcg gcg aac cag ttg 624 Ala Ala Ala Val Glu Glu Ala Ser Asp Thr Ala Ala Ala Asn Gln Leu 195 200 205 atg aac aat gtg ccc cag gcg ctg caa cag ctg gcc cag ccc acg cag 672 Met Asn Asn Val Pro Gln Ala Leu Gln Gln Leu Ala Gln Pro Thr Gln 210 215 220 ggc acc acg cct tct tcc aag ctg ggt ggc ctg tgg aag acg gtc tcg 720 Gly Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu Trp Lys Thr Val Ser 225 230 235 240 ccg cat cgg tcg ccg atc agc aac atg gtg tcg atg gcc aac aac cac 768 Pro His Arg Ser Pro Ile Ser Asn Met Val Ser Met Ala Asn Asn His 245 250 255 atg tcg atg acc aac tcg ggt gtg tcg atg acc aac acc ttg agc tcg 816 Met Ser Met Thr Asn Ser Gly Val Ser Met Thr Asn Thr Leu Ser Ser 260 265 270 atg ttg aag ggc ttt gct ccg gcg gcg gcc gcc cag gcc gtg caa acc 864 Met Leu Lys Gly Phe Ala Pro Ala Ala Ala Ala Gln Ala Val Gln Thr 275 280 285 gcg gcg caa aac ggg gtc cgg gcg atg agc tcg ctg ggc agc tcg ctg 912 Ala Ala Gln Asn Gly Val Arg Ala Met Ser Ser Leu Gly Ser Ser Leu 290 295 300 ggt tct tcg ggt ctg ggc ggt ggg gtg gcc gcc aac ttg ggt cgg gcg 960 Gly Ser Ser Gly Leu Gly Gly Gly Val Ala Ala Asn Leu Gly Arg Ala 305 310 315 320 gcc tcg gtc ggt tcg ttg tcg gtg ccg cag gcc tgg gcc gcg gcc aac 1008 Ala Ser Val Gly Ser Leu Ser Val Pro Gln Ala Trp Ala Ala Ala Asn 325 330 335 cag gca gtc acc ccg gcg gcg cgg gcg ctg ccg ctg acc agc ctg acc 1056 Gln Ala Val Thr Pro Ala Ala Arg Ala Leu Pro Leu Thr Ser Leu Thr 340 345 350 agc gcc gcg gaa aga ggg ccc ggg cag atg ctg ggc ggg ctg ccg gtg 1104 Ser Ala Ala Glu Arg Gly Pro Gly Gln Met Leu Gly Gly Leu Pro Val 355 360 365 ggg cag atg ggc gcc agg gcc ggt ggt ggg ctc agt ggt gtg ctg cgt 1152 Gly Gln Met Gly Ala Arg Ala Gly Gly Gly Leu Ser Gly Val Leu Arg 370 375 380 gtt ccg ccg cga ccc tat gtg atg ccg cat tct ccg gca gcc ggc gat 1200 Val Pro Pro Arg Pro Tyr Val Met Pro His Ser Pro Ala Ala Gly Asp 385 390 395 400 atc gcc ccg ccg gcc ttg tcg cag gac cgg ttc gcc gac ttc ccc gcg 1248 Ile Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe Ala Asp Phe Pro Ala 405 410 415 ctg ccc ctc gac ccg tcc gcg atg gtc gcc caa gtg ggg cca cag gtg 1296 Leu Pro Leu Asp Pro Ser Ala Met Val Ala Gln Val Gly Pro Gln Val 420 425 430 gtc aac atc aac acc aaa ctg ggc tac aac aac gcc gtg ggc gcc ggg 1344 Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn Ala Val Gly Ala Gly 435 440 445 acc ggc atc gtc atc gat ccc aac ggt gtc gtg ctg acc aac aac cac 1392 Thr Gly Ile Val Ile Asp Pro Asn Gly Val Val Leu Thr Asn Asn His 450 455 460 gtg atc gcg ggc gcc acc gac atc aat gcg ttc agc gtc ggc tcc ggc 1440 Val Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe Ser Val Gly Ser Gly 465 470 475 480 caa acc tac ggc gtc gat gtg gtc ggg tat gac cgc acc cag gat gtc 1488 Gln Thr Tyr Gly Val Asp Val Val Gly Tyr Asp Arg Thr Gln Asp Val 485 490 495 gcg gtg ctg cag ctg cgc ggt gcc ggt ggc ctg ccg tcg gcg gcg atc 1536 Ala Val Leu Gln Leu Arg Gly Ala Gly Gly Leu Pro Ser Ala Ala Ile 500 505 510 ggt ggc ggc gtc gcg gtt ggt gag ccc gtc gtc gcg atg ggc aac agc 1584 Gly Gly Gly Val Ala Val Gly Glu Pro Val Val Ala Met Gly Asn Ser 515 520 525 ggt ggg cag ggc gga acg ccc cgt gcg gtg cct ggc agg gtg gtc gcg 1632 Gly Gly Gln Gly Gly Thr Pro Arg Ala Val Pro Gly Arg Val Val Ala 530 535 540 ctc ggc caa acc gtg cag gcg tcg gat tcg ctg acc ggt gcc gaa gag 1680 Leu Gly Gln Thr Val Gln Ala Ser Asp Ser Leu Thr Gly Ala Glu Glu 545 550 555 560 aca ttg aac ggg ttg atc cag ttc gat gcc gcg atc cag ccc ggt gat 1728 Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala Ile Gln Pro Gly Asp 565 570 575 tcg ggc ggg ccc gtc gtc aac ggc cta gga cag gtg gtc ggt atg aac 1776 Ser Gly Gly Pro Val Val Asn Gly Leu Gly Gln Val Val Gly Met Asn 580 585 590 acg gcc gcg tcc tag gatatc 1797 Thr Ala Ala Ser 595 20 596 PRT Artificial Sequence Description of Artificial Sequencebi-fusion protein TbH9-Ra35 (designated MTB59F) 20 His Met His His His His His His Met Val Asp Phe Gly Ala Leu Pro 1 5 10 15 Pro Glu Ile Asn Ser Ala Arg Met Tyr Ala Gly Pro Gly Ser Ala Ser 20 25 30 Leu Val Ala Ala Ala Gln Met Trp Asp Ser Val Ala Ser Asp Leu Phe 35 40 45 Ser Ala Ala Ser Ala Phe Gln Ser Val Val Trp Gly Leu Thr Val Gly 50 55 60 Ser Trp Ile Gly Ser Ser Ala Gly Leu Met Val Ala Ala Ala Ser Pro 65 70 75 80 Tyr Val Ala Trp Met Ser Val Thr Ala Gly Gln Ala Glu Leu Thr Ala 85 90 95 Ala Gln Val Arg Val Ala Ala Ala Ala Tyr Glu Thr Ala Tyr Gly Leu 100 105 110 Thr Val Pro Pro Pro Val Ile Ala Glu Asn Arg Ala Glu Leu Met Ile 115 120 125 Leu Ile Ala Thr Asn Leu Leu Gly Gln Asn Thr Pro Ala Ile Ala Val 130 135 140 Asn Glu Ala Glu Tyr Gly Glu Met Trp Ala Gln Asp Ala Ala Ala Met 145 150 155 160 Phe Gly Tyr Ala Ala Ala Thr Ala Thr Ala Thr Ala Thr Leu Leu Pro 165 170 175 Phe Glu Glu Ala Pro Glu Met Thr Ser Ala Gly Gly Leu Leu Glu Gln 180 185 190 Ala Ala Ala Val Glu Glu Ala Ser Asp Thr Ala Ala Ala Asn Gln Leu 195 200 205 Met Asn Asn Val Pro Gln Ala Leu Gln Gln Leu Ala Gln Pro Thr Gln 210 215 220 Gly Thr Thr Pro Ser Ser Lys Leu Gly Gly Leu Trp Lys Thr Val Ser 225 230 235 240 Pro His Arg Ser Pro Ile Ser Asn Met Val Ser Met Ala Asn Asn His 245 250 255 Met Ser Met Thr Asn Ser Gly Val Ser Met Thr Asn Thr Leu Ser Ser 260 265 270 Met Leu Lys Gly Phe Ala Pro Ala Ala Ala Ala Gln Ala Val Gln Thr 275 280 285 Ala Ala Gln Asn Gly Val Arg Ala Met Ser Ser Leu Gly Ser Ser Leu 290 295 300 Gly Ser Ser Gly Leu Gly Gly Gly Val Ala Ala Asn Leu Gly Arg Ala 305 310 315 320 Ala Ser Val Gly Ser Leu Ser Val Pro Gln Ala Trp Ala Ala Ala Asn 325 330 335 Gln Ala Val Thr Pro Ala Ala Arg Ala Leu Pro Leu Thr Ser Leu Thr 340 345 350 Ser Ala Ala Glu Arg Gly Pro Gly Gln Met Leu Gly Gly Leu Pro Val 355 360 365 Gly Gln Met Gly Ala Arg Ala Gly Gly Gly Leu Ser Gly Val Leu Arg 370 375 380 Val Pro Pro Arg Pro Tyr Val Met Pro His Ser Pro Ala Ala Gly Asp 385 390 395 400 Ile Ala Pro Pro Ala Leu Ser Gln Asp Arg Phe Ala Asp Phe Pro Ala 405 410 415 Leu Pro Leu Asp Pro Ser Ala Met Val Ala Gln Val Gly Pro Gln Val 420 425 430 Val Asn Ile Asn Thr Lys Leu Gly Tyr Asn Asn Ala Val Gly Ala Gly 435 440 445 Thr Gly Ile Val Ile Asp Pro Asn Gly Val Val Leu Thr Asn Asn His 450 455 460 Val Ile Ala Gly Ala Thr Asp Ile Asn Ala Phe Ser Val Gly Ser Gly 465 470 475 480 Gln Thr Tyr Gly Val Asp Val Val Gly Tyr Asp Arg Thr Gln Asp Val 485 490 495 Ala Val Leu Gln Leu Arg Gly Ala Gly Gly Leu Pro Ser Ala Ala Ile 500 505 510 Gly Gly Gly Val Ala Val Gly Glu Pro Val Val Ala Met Gly Asn Ser 515 520 525 Gly Gly Gln Gly Gly Thr Pro Arg Ala Val Pro Gly Arg Val Val Ala 530 535 540 Leu Gly Gln Thr Val Gln Ala Ser Asp Ser Leu Thr Gly Ala Glu Glu 545 550 555 560 Thr Leu Asn Gly Leu Ile Gln Phe Asp Ala Ala Ile Gln Pro Gly Asp 565 570 575 Ser Gly Gly Pro Val Val Asn Gly Leu Gly Gln Val Val Gly Met Asn 580 585 590 Thr Ala Ala Ser 595 21 500 DNA Mycobacterium tuberculosis MTB8.4 (DPV) cDNA 21 cgtggcaatg tcgttgaccg tcggggccgg ggtcgcctcc gcagatcccg tggacgcggt 60 cattaacacc acctgcaatt acgggcaggt agtagctgcg ctcaacgcga cggatccggg 120 ggctgccgca cagttcaacg cctcaccggt ggcgcagtcc tatttgcgca atttcctcgc 180 cgcaccgcca cctcagcgcg ctgccatggc cgcgcaattg caagctgtgc cgggggcggc 240 acagtacatc ggccttgtcg agtcggttgc cggctcctgc aacaactatt aagcccatgc 300 gggccccatc ccgcgacccg gcatcgtcgc cggggctagg ccagattgcc ccgctcctca 360 acgggccgca tcccgcgacc cggcatcgtc gccggggcta ggccagattg ccccgctcct 420 caacgggccg catctcgtgc cgaattcctg cagcccgggg gatccactag ttctagagcg 480 gccgccaccg cggtggagct 500 22 96 PRT Mycobacterium tuberculosis MTB8.4 (DPV) 22 Val Ala Met Ser Leu Thr Val Gly Ala Gly Val Ala Ser Ala Asp Pro 1 5 10 15 Val Asp Ala Val Ile Asn Thr Thr Cys Asn Tyr Gly Gln Val Val Ala 20 25 30 Ala Leu Asn Ala Thr Asp Pro Gly Ala Ala Ala Gln Phe Asn Ala Ser 35 40 45 Pro Val Ala Gln Ser Tyr Leu Arg Asn Phe Leu Ala Ala Pro Pro Pro 50 55 60 Gln Arg Ala Ala Met Ala Ala Gln Leu Gln Ala Val Pro Gly Ala Ala 65 70 75 80 Gln Tyr Ile Gly Leu Val Glu Ser Val Ala Gly Ser Cys Asn Asn Tyr 85 90 95 23 585 DNA Mycobacterium tuberculosis MTB9.8 (MSL) 23 tggattccga tagcggtttc ggcccctcga cgggcgacca cggcgcgcag gcctccgaac 60 ggggggccgg gacgctggga ttcgccggga ccgcaaccaa agaacgccgg gtccgggcgg 120 tcgggctgac cgcactggcc ggtgatgagt tcggcaacgg cccccggatg ccgatggtgc 180 cggggacctg ggagcagggc agcaacgagc ccgaggcgcc cgacggatcg gggagagggg 240 gaggcgacgg cttaccgcac gacagcaagt aaccgaattc cgaatcacgt ggacccgtac 300 gggtcgaaag gagagatgtt atgagccttt tggatgctca tatcccacag ttggtggcct 360 cccagtcggc gtttgccgcc aaggcggggc tgatgcggca cacgatcggt caggccgagc 420 aggcggcgat gtcggctcag gcgtttcacc agggggagtc gtcggcggcg tttcaggccg 480 cccatgcccg gtttgtggcg gcggccgcca aagtcaacac cttgttggat gtcgcgcagg 540 cgaatctggg tgaggccgcc ggtacctatg tggccgccga tgctg 585 24 97 PRT Mycobacterium tuberculosis MTB9.8 (MSL) 24 Met Ser Leu Leu Asp Ala His Ile Pro Gln Leu Val Ala Ser Gln Ser 1 5 10 15 Ala Phe Ala Ala Lys Ala Gly Leu Met Arg His Thr Ile Gly Gln Ala 20 25 30 Glu Gln Ala Ala Met Ser Ala Gln Ala Phe His Gln Gly Glu Ser Ser 35 40 45 Ala Ala Phe Gln Ala Ala His Ala Arg Phe Val Ala Ala Ala Ala Lys 50 55 60 Val Asn Thr Leu Leu Asp Val Ala Gln Ala Asn Leu Gly Glu Ala Ala 65 70 75 80 Gly Thr Tyr Val Ala Ala Asp Ala Ala Ala Ala Ser Thr Tyr Thr Gly 85 90 95 Phe 25 1742 DNA Mycobacterium tuberculosis MTB9.9A (MTI, also known as MTI-A) 25 ccgctctctt tcaacgtcat aagttcggtg ggccagtcgg ccgcgcgtgc atatggcacc 60 aataacgcgt gtcccatgga tacccggacc gcacgacggt agagcggatc agcgcagccg 120 gtgccgaaca ctaccgcgtc cacgctcagc cctgccgcgt tgcggaagat cgagcccagg 180 ttctcatggt cgttaacgcc ttccaacact gcgacggtgc gcgccccggc gaccacctga 240 gcaacgctcg gctccggcac ccggcgcgcg gctgccaaca ccccacgatt gagatggaag 300 ccgatcaccc gtgccatgac atcagccgac gctcgatagt acggcgcgcc gacaccggcc 360 agatcatcct tgagctcggc cagccggcgg tcggtgccga acagcgccag cggcgtgaac 420 cgtgaggcca gcatgcgctg caccaccagc acaccctcgg cgatcaccaa cgccttgccg 480 gtcggcagat cgggacnacn gtcgatgctg ttcaggtcac ggaaatcgtc gagccgtggg 540 tcgtcgggat cgcagacgtc ctgaacatcg aggccgtcgg ggtgctgggc acaacggcct 600 tcggtcacgg gctttcgtcg accagagcca gcatcagatc ggcggcgctg cgcaggatgt 660 cacgctcgct gcggttcagc gtcgcgagcc gctcagccag ccactcttgc agagagccgt 720 tgctgggatt aattgggaga ggaagacagc atgtcgttcg tgaccacaca gccggaagcc 780 ctggcagctg cggcggcgaa cctacagggt attggcacga caatgaacgc ccagaacgcg 840 gccgcggctg ctccaaccac cggagtagtg cccgcagccg ccgatgaagt atcagcgctg 900 accgcggctc agtttgctgc gcacgcgcag atgtaccaaa cggtcagcgc ccaggccgcg 960 gccattcacg aaatgttcgt gaacacgctg gtggccagtt ctggctcata cgcggccacc 1020 gaggcggcca acgcagccgc tgccggctga acgggctcgc acgaacctgc tgaaggagag 1080 ggggaacatc cggagttctc gggtcagggg ttgcgccagc gcccagccga ttcagntatc 1140 ggcgtccata acagcagacg atctaggcat tcagtactaa ggagacaggc aacatggcct 1200 cacgttttat gacggatccg catgcgatgc gggacatggc gggccgtttt gaggtgcacg 1260 cccagacggt ggaggacgag gctcgccgga tgtgggcgtc cgcgcaaaac atttccggtg 1320 cgggctggag tggcatggcc gaggcgacct cgctagacac catgacctag atgaatcagg 1380 cgtttcgcaa catcgtgaac atgctgcacg gggtgcgtga cgggctggtt cgcgacgcca 1440 acaantacga acagcaagag caggcctccc agcagatcct gagcagntag cgccgaaagc 1500 cacagctgng tacgntttct cacattagga gaacaccaat atgacgatta attaccagtt 1560 cggggacgtc gacgctcatg gcgccatgat ccgcgctcag gcggcgtcgc ttgaggcgga 1620 gcatcaggcc atcgttcgtg atgtgttggc cgcgggtgac ttttggggcg gcgccggttc 1680 ggtggcttgc caggagttca ttacccagtt gggccgtaac ttccaggtga tctacgagca 1740 gg 1742 26 2836 DNA Mycobacterium tuberculosis MTB9.9A (MTI also known as MTI-A) 26 gttgattccg ttcgcggcgc cgccgaagac caccaactcc gctggggtgg tcgcacaggc 60 ggttgcgtcg gtcagctggc cgaatcccaa tgattggtgg ctcngtgcgg ttgctgggct 120 cgattacccc cacggaaagg acgacgatcg ttcgtttgct cggtcagtcg tacttggcga 180 cgggcatggc gcggtttctt acctcgatcg cacagcagct gaccttcggc ccagggggca 240 caacggctgg ctccggcgga gcctggtacc caacgccaca attcgccggc ctgggtgcag 300 gcccggcggt gtcggcgagt ttggcgcggg cggagccggt cgggaggttg tcggtgccgc 360 caagttgggc cgtcgcggct ccggccttcg cggagaagcc tgaggcgggc acgccgatgt 420 ccgtcatcgg cgaagcgtcc agctgcggtc agggaggcct gcttcgaggc ataccgctgg 480 cgagagcggg gcggcgtaca ggcgccttcg ctcaccgata cgggttccgc cacagcgtga 540 ttacccggtc tccgtcggcg ggatagcttt cgatccggtc tgcgcggccg ccggaaatgc 600 tgcagatagc gatcgaccgc gccggtcggt aaacgccgca cacggcacta tcaatgcgca 660 cggcgggcgt tgatgccaaa ttgaccgtcc cgacggggct ttatctgcgg caagatttca 720 tccccagccc ggtcggtggg ccgataaata cgctggtcag cgcgactctt ccggctgaat 780 tcgatgctct gggcgcccgc tcgacgccga gtatctcgag tgggccgcaa acccggtcaa 840 acgctgttac tgtggcgtta ccacaggtga atttgcggtg ccaactggtg aacacttgcg 900 aacgggtggc atcgaaatca acttgttgcg ttgcagtgat ctactctctt gcagagagcc 960 gttgctggga ttaattggga gaggaagaca gcatgtcgtt cgtgaccaca cagccggaag 1020 ccctggcagc tgcggcggcg aacctacagg gtattggcac gacaatgaac gcccagaacg 1080 cggccgcggc tgctccaacc accggagtag tgcccgcagc cgccgatgaa gtatcagcgc 1140 tgaccgcggc tcagtttgct gcgcacgcgc agatgtacca aacggtcagc gcccaggccg 1200 cggccattca cgaaatgttc gtgaacacgc tggtggccag ttctggctca tacgcggcca 1260 ccgaggcggc caacgcagcc gctgccggct gaacgggctc gcacgaacct gctgaaggag 1320 agggggaaca tccggagttc tcgggtcagg ggttgcgcca gcgcccagcc gattcagcta 1380 tcggcgtcca taacagcaga cgatctaggc attcagtact aaggagacag gcaacatggc 1440 ctcacgtttt atgacggatc cgcatgcgat gcgggacatg gcgggccgtt ttgaggtgca 1500 cgcccagacg gtggaggacg aggctcgccg gatgtgggcg tccgcgcaaa acatttccgg 1560 tgcgggctgg agtggcatgg ccgaggcgac ctcgctagac accatgacct agatgaatca 1620 ggcgtttcgc aacatcgtga acatgctgca cggggtgcgt gacgggctgg ttcgcgacgc 1680 caacaactac gaacagcaag agcaggcctc ccagcagatc ctgagcagct agcgccgaaa 1740 gccacagctg cgtacgcttt ctcacattag gagaacacca atatgacgat taattaccag 1800 ttcggggacg tcgacgctca tggcgccatg atccgcgctc aggcggcgtc gcttgaggcg 1860 gagcatcagg ccatcgttcg tgatgtgttg gccgcgggtg acttttgggg cggcgccggt 1920 tcggtggctt gccaggagtt cattacccag ttgggccgta acttccaggt gatctacgag 1980 caggccaacg cccacgggca gaaggtgcag gctgccggca acaacatggc gcaaaccgac 2040 agcgccgtcg gctccagctg ggcctaaaac tgaacttcag tcgcggcagc acaccaacca 2100 gccggtgtgc tgctgtgtcc tgcagttaac tagcactcga ccgctgaggt agcgatggat 2160 caacagagta cccgcaccga catcaccgtc aacgtcgacg gcttctggat gcttcaggcg 2220 ctactggata tccgccacgt tgcgcctgag ttacgttgcc ggccgtacgt ctccaccgat 2280 tccaatgact ggctaaacga gcacccgggg atggcggtca tgcgcgagca gggcattgtc 2340 gtcaacgacg cggtcaacga acaggtcgct gcccggatga aggtgcttgc cgcacctgat 2400 cttgaagtcg tcgccctgct gtcacgcggc aagttgctgt acggggtcat agacgacgag 2460 aaccagccgc cgggttcgcg tgacatccct gacaatgagt tccgggtggt gttggcccgg 2520 cgaggccagc actgggtgtc ggcggtacgg gttggcaatg acatcaccgt cgatgacgtg 2580 acggtctcgg atagcgcctc gatcgccgca ctggtaatgg acggtctgga gtcgattcac 2640 cacgccgacc cagccgcgat caacgcggtc aacgtgccaa tggaggagat ctcgtgccga 2700 attcggcacg aggcacgagg cggtgtcggt gacgacggga tcgatcacga tcatcgaccg 2760 gccgggatcc ttggcgatct cgttgagcac gacccgggcc cgcgggaagc tctgcgacat 2820 ccatgggttc ttcccg 2836 27 94 PRT Mycobacterium tuberculosis MTB9.9A (MTI, also known as MTI-A) ORF peptide 27 Met Thr Ile Asn Tyr Gln Phe Gly Asp Val Asp Ala His Gly Ala Met 1 5 10 15 Ile Arg Ala Leu Ala Gly Leu Leu Glu Ala Glu His Gln Ala Ile Ile 20 25 30 Ser Asp Val Leu Thr Ala Ser Asp Phe Trp Gly Gly Ala Gly Ser Ala 35 40 45 Ala Cys Gln Gly Phe Ile Thr Gln Leu Gly Arg Asn Phe Gln Val Ile 50 55 60 Tyr Glu Gln Ala Asn Ala His Gly Gln Lys Val Gln Ala Ala Gly Asn 65 70 75 80 Asn Met Ala Gln Thr Asp Ser Ala Val Gly Ser Ser Trp Ala 85 90 28 1200 DNA Mycobacterium tuberculosis MTB40 (HTCC#1) cDNA 28 caggcatgag cagagcgttc atcatcgatc caacgatcag tgccattgac ggcttgtacg 60 accttctggg gattggaata cccaaccaag ggggtatcct ttactcctca ctagagtact 120 tcgaaaaagc cctggaggag ctggcagcag cgtttccggg tgatggctgg ttaggttcgg 180 ccgcggacaa atacgccggc aaaaaccgca accacgtgaa ttttttccag gaactggcag 240 acctcgatcg tcagctcatc agcctgatcc acgaccaggc caacgcggtc cagacgaccc 300 gcgacatcct ggagggcgcc aagaaaggtc tcgagttcgt gcgcccggtg gctgtggacc 360 tgacctacat cccggtcgtc gggcacgccc tatcggccgc cttccaggcg ccgttttgcg 420 cgggcgcgat ggccgtagtg ggcggcgcgc ttgcctactt ggtcgtgaaa acgctgatca 480 acgcgactca actcctcaaa ttgcttgcca aattggcgga gttggtcgcg gccgccattg 540 cggacatcat ttcggatgtg gcggacatca tcaagggcac cctcggagaa gtgtgggagt 600 tcatcacaaa cgcgctcaac ggcctgaaag agctttggga caagctcacg gggtgggtga 660 ccggactgtt ctctcgaggg tggtcgaacc tggagtcctt ctttgcgggc gtccccggct 720 tgaccggcgc gaccagcggc ttgtcgcaag tgactggctt gttcggtgcg gccggtctgt 780 ccgcatcgtc gggcttggct cacgcggata gcctggcgag ctcagccagc ttgcccgccc 840 tggccggcat tgggggcggg tccggttttg ggggcttgcc gagcctggct caggtccatg 900 ccgcctcaac tcggcaggcg ctacggcccc gagctgatgg cccggtcggc gccgctgccg 960 agcaggtcgg cgggcagtcg cagctggtct ccgcgcaggg ttcccaaggt atgggcggac 1020 ccgtaggcat gggcggcatg cacccctctt cgggggcgtc gaaagggacg acgacgaaga 1080 agtactcgga aggcgcggcg gcgggcactg aagacgccga gcgcgcgcca gtcgaagctg 1140 acgcgggcgg tgggcaaaag gtgctggtac gaaacgtcgt ctaacggcat ggcgagccaa 1200 29 392 PRT Mycobacterium tuberculosis MTB40 (HTCC#1) 29 Met Ser Arg Ala Phe Ile Ile Asp Pro Thr Ile Ser Ala Ile Asp Gly 1 5 10 15 Leu Tyr Asp Leu Leu Gly Ile Gly Ile Pro Asn Gln Gly Gly Ile Leu 20 25 30 Tyr Ser Ser Leu Glu Tyr Phe Glu Lys Ala Leu Glu Glu Leu Ala Ala 35 40 45 Ala Phe Pro Gly Asp Gly Trp Leu Gly Ser Ala Ala Asp Lys Tyr Ala 50 55 60 Gly Lys Asn Arg Asn His Val Asn Phe Phe Gln Glu Leu Ala Asp Leu 65 70 75 80 Asp Arg Gln Leu Ile Ser Leu Ile His Asp Gln Ala Asn Ala Val Gln 85 90 95 Thr Thr Arg Asp Ile Leu Glu Gly Ala Lys Lys Gly Leu Glu Phe Val 100 105 110 Arg Pro Val Ala Val Asp Leu Thr Tyr Ile Pro Val Val Gly His Ala 115 120 125 Leu Ser Ala Ala Phe Gln Ala Pro Phe Cys Ala Gly Ala Met Ala Val 130 135 140 Val Gly Gly Ala Leu Ala Tyr Leu Val Val Lys Thr Leu Ile Asn Ala 145 150 155 160 Thr Gln Leu Leu Lys Leu Leu Ala Lys Leu Ala Glu Leu Val Ala Ala 165 170 175 Ala Ile Ala Asp Ile Ile Ser Asp Val Ala Asp Ile Ile Lys Gly Thr 180 185 190 Leu Gly Glu Val Trp Glu Phe Ile Thr Asn Ala Leu Asn Gly Leu Lys 195 200 205 Glu Leu Trp Asp Lys Leu Thr Gly Trp Val Thr Gly Leu Phe Ser Arg 210 215 220 Gly Trp Ser Asn Leu Glu Ser Phe Phe Ala Gly Val Pro Gly Leu Thr 225 230 235 240 Gly Ala Thr Ser Gly Leu Ser Gln Val Thr Gly Leu Phe Gly Ala Ala 245 250 255 Gly Leu Ser Ala Ser Ser Gly Leu Ala His Ala Asp Ser Leu Ala Ser 260 265 270 Ser Ala Ser Leu Pro Ala Leu Ala Gly Ile Gly Gly Gly Ser Gly Phe 275 280 285 Gly Gly Leu Pro Ser Leu Ala Gln Val His Ala Ala Ser Thr Arg Gln 290 295 300 Ala Leu Arg Pro Arg Ala Asp Gly Pro Val Gly Ala Ala Ala Glu Gln 305 310 315 320 Val Gly Gly Gln Ser Gln Leu Val Ser Ala Gln Gly Ser Gln Gly Met 325 330 335 Gly Gly Pro Val Gly Met Gly Gly Met His Pro Ser Ser Gly Ala Ser 340 345 350 Lys Gly Thr Thr Thr Lys Lys Tyr Ser Glu Gly Ala Ala Ala Gly Thr 355 360 365 Glu Asp Ala Glu Arg Ala Pro Val Glu Ala Asp Ala Gly Gly Gly Gln 370 375 380 Lys Val Leu Val Arg Asn Val Val 385 390 30 1441 DNA Mycobacterium tuberculosis MTB41 (MTCC#2) cDNA 30 gaggttgctg gcaatggatt tcgggctttt acctccggaa gtgaattcaa gccgaatgta 60 ttccggtccg gggccggagt cgatgctagc cgccgcggcc gcctgggacg gtgtggccgc 120 ggagttgact tccgccgcgg tctcgtatgg atcggtggtg tcgacgctga tcgttgagcc 180 gtggatgggg ccggcggcgg ccgcgatggc ggccgcggca acgccgtatg tggggtggct 240 ggccgccacg gcggcgctgg cgaaggagac ggccacacag gcgagggcag cggcggaagc 300 gtttgggacg gcgttcgcga tgacggtgcc accatccctc gtcgcggcca accgcagccg 360 gttgatgtcg ctggtcgcgg cgaacattct ggggcaaaac agtgcggcga tcgcggctac 420 ccaggccgag tatgccgaaa tgtgggccca agacgctgcc gtgatgtaca gctatgaggg 480 ggcatctgcg gccgcgtcgg cgttgccgcc gttcactcca cccgtgcaag gcaccggccc 540 ggccgggccc gcggccgcag ccgcggcgac ccaagccgcc ggtgcgggcg ccgttgcgga 600 tgcacaggcg acactggccc agctgccccc ggggatcctg agcgacattc tgtccgcatt 660 ggccgccaac gctgatccgc tgacatcggg actgttgggg atcgcgtcga ccctcaaccc 720 gcaagtcgga tccgctcagc cgatagtgat ccccaccccg ataggggaat tggacgtgat 780 cgcgctctac attgcatcca tcgcgaccgg cagcattgcg ctcgcgatca cgaacacggc 840 cagaccctgg cacatcggcc tatacgggaa cgccggcggg ctgggaccga cgcagggcca 900 tccactgagt tcggcgaccg acgagccgga gccgcactgg ggccccttcg ggggcgcggc 960 gccggtgtcc gcgggcgtcg gccacgcagc attagtcgga gcgttgtcgg tgccgcacag 1020 ctggaccacg gccgccccgg agatccagct cgccgttcag gcaacaccca ccttcagctc 1080 cagcgccggc gccgacccga cggccctaaa cgggatgccg gcaggcctgc tcagcgggat 1140 ggctttggcg agcctggccg cacgcggcac gacgggcggt ggcggcaccc gtagcggcac 1200 cagcactgac ggccaagagg acggccgcaa acccccggta gttgtgatta gagagcagcc 1260 gccgcccgga aaccccccgc ggtaaaagtc cggcaaccgt tcgtcgccgc gcggaaaatg 1320 cctggtgagc gtggctatcc gacgggccgt tcacaccgct tgtagtagcg tacggctatg 1380 gacgacggtg tctggattct cggcggctat cagagcgatt ttgctcgcaa cctcagcaaa 1440 g 1441 31 423 PRT Mycobacterium tuberculosis MTB41 (MTCC#2) 31 Met Asp Phe Gly Leu Leu Pro Pro Glu Val Asn Ser Ser Arg Met Tyr 1 5 10 15 Ser Gly Pro Gly Pro Glu Ser Met Leu Ala Ala Ala Ala Ala Trp Asp 20 25 30 Gly Val Ala Ala Glu Leu Thr Ser Ala Ala Val Ser Tyr Gly Ser Val 35 40 45 Val Ser Thr Leu Ile Val Glu Pro Trp Met Gly Pro Ala Ala Ala Ala 50 55 60 Met Ala Ala Ala Ala Thr Pro Tyr Val Gly Trp Leu Ala Ala Thr Ala 65 70 75 80 Ala Leu Ala Lys Glu Thr Ala Thr Gln Ala Arg Ala Ala Ala Glu Ala 85 90 95 Phe Gly Thr Ala Phe Ala Met Thr Val Pro Pro Ser Leu Val Ala Ala 100 105 110 Asn Arg Ser Arg Leu Met Ser Leu Val Ala Ala Asn Ile Leu Gly Gln 115 120 125 Asn Ser Ala Ala Ile Ala Ala Thr Gln Ala Glu Tyr Ala Glu Met Trp 130 135 140 Ala Gln Asp Ala Ala Val Met Tyr Ser Tyr Glu Gly Ala Ser Ala Ala 145 150 155 160 Ala Ser Ala Leu Pro Pro Phe Thr Pro Pro Val Gln Gly Thr Gly Pro 165 170 175 Ala Gly Pro Ala Ala Ala Ala Ala Ala Thr Gln Ala Ala Gly Ala Gly 180 185 190 Ala Val Ala Asp Ala Gln Ala Thr Leu Ala Gln Leu Pro Pro Gly Ile 195 200 205 Leu Ser Asp Ile Leu Ser Ala Leu Ala Ala Asn Ala Asp Pro Leu Thr 210 215 220 Ser Gly Leu Leu Gly Ile Ala Ser Thr Leu Asn Pro Gln Val Gly Ser 225 230 235 240 Ala Gln Pro Ile Val Ile Pro Thr Pro Ile Gly Glu Leu Asp Val Ile 245 250 255 Ala Leu Tyr Ile Ala Ser Ile Ala Thr Gly Ser Ile Ala Leu Ala Ile 260 265 270 Thr Asn Thr Ala Arg Pro Trp His Ile Gly Leu Tyr Gly Asn Ala Gly 275 280 285 Gly Leu Gly Pro Thr Gln Gly His Pro Leu Ser Ser Ala Thr Asp Glu 290 295 300 Pro Glu Pro His Trp Gly Pro Phe Gly Gly Ala Ala Pro Val Ser Ala 305 310 315 320 Gly Val Gly His Ala Ala Leu Val Gly Ala Leu Ser Val Pro His Ser 325 330 335 Trp Thr Thr Ala Ala Pro Glu Ile Gln Leu Ala Val Gln Ala Thr Pro 340 345 350 Thr Phe Ser Ser Ser Ala Gly Ala Asp Pro Thr Ala Leu Asn Gly Met 355 360 365 Pro Ala Gly Leu Leu Ser Gly Met Ala Leu Ala Ser Leu Ala Ala Arg 370 375 380 Gly Thr Thr Gly Gly Gly Gly Thr Arg Ser Gly Thr Ser Thr Asp Gly 385 390 395 400 Gln Glu Asp Gly Arg Lys Pro Pro Val Val Val Ile Arg Glu Gln Pro 405 410 415 Pro Pro Gly Asn Pro Pro Arg 420 32 154 DNA Mycobacterium tuberculosis ESAT-6 32 atgacagagc agcagtggaa tttcgcgggt atcgaggccg cggcaagcgc aatccaggga 60 aatgtcacgt ccattcattc cctccttgac gaggggaagc agtccctgac caagctcgca 120 gcggcctggg gcggtagcgg ttcggaagcg tacc 154 33 51 PRT Mycobacterium tuberculosis ESAT-6 33 Met Thr Glu Gln Gln Trp Asn Phe Ala Gly Ile Glu Ala Ala Ala Ser 1 5 10 15 Ala Ile Gln Gly Asn Val Thr Ser Ile His Ser Leu Leu Asp Glu Gly 20 25 30 Lys Gln Ser Leu Thr Lys Leu Ala Ala Ala Trp Gly Gly Ser Gly Ser 35 40 45 Glu Ala Tyr 50 34 327 DNA Mycobacterium tuberculosis Tb38-1 or 38-1 (MTb11) 34 cggcacgaga gaccgatgcc gctaccctcg cgcaggaggc aggtaatttc gagcggatct 60 ccggcgacct gaaaacccag atcgaccagg tggagtcgac ggcaggttcg ttgcagggcc 120 agtggcgcgg cgcggcgggg acggccgccc aggccgcggt ggtgcgcttc caagaagcag 180 ccaataagca gaagcaggaa ctcgacgaga tctcgacgaa tattcgtcag gccggcgtcc 240 aatactcgag ggccgacgag gagcagcagc aggcgctgtc ctcgcaaatg ggcttctgac 300 ccgctaatac gaaaagaaac ggagcaa 327 35 95 PRT Mycobacterium tuberculosis Tb38-1 or 38-1 (MTb11) 35 Thr Asp Ala Ala Thr Leu Ala Gln Glu Ala Gly Asn Phe Glu Arg Ile 1 5 10 15 Ser Gly Asp Leu Lys Thr Gln Ile Asp Gln Val Glu Ser Thr Ala Gly 20 25 30 Ser Leu Gln Gly Gln Trp Arg Gly Ala Ala Gly Thr Ala Ala Gln Ala 35 40 45 Ala Val Val Arg Phe Gln Glu Ala Ala Asn Lys Gln Lys Gln Glu Leu 50 55 60 Asp Glu Ile Ser Thr Asn Ile Arg Gln Ala Gly Val Gln Tyr Ser Arg 65 70 75 80 Ala Asp Glu Glu Gln Gln Gln Ala Leu Ser Ser Gln Met Gly Phe 85 90 95 36 542 DNA Mycobacterium tuberculosis TbRa3 36 gaattcggca cgagaggtga tcgacatcat cgggaccagc cccacatcct gggaacaggc 60 ggcggcggag gcggtccagc gggcgcggga tagcgtcgat gacatccgcg tcgctcgggt 120 cattgagcag gacatggccg tggacagcgc cggcaagatc acctaccgca tcaagctcga 180 agtgtcgttc aagatgaggc cggcgcaacc gcgctagcac gggccggcga gcaagacgca 240 aaatcgcacg gtttgcggtt gattcgtgcg attttgtgtc tgctcgccga ggcctaccag 300 gcgcggccca ggtccgcgtg ctgccgtatc caggcgtgca tcgcgattcc ggcggccacg 360 ccggagttaa tgcttcgcgt cgacccgaac tgggcgatcc gccggngagc tgatcgatga 420 ccgtggccag cccgtcgatg cccgagttgc ccgaggaaac gtgctgccag gccggtagga 480 agcgtccgta ggcggcggtg ctgaccggct ctgcctgcgc cctcagtgcg gccagcgagc 540 gg 542 37 66 PRT Mycobacterium tuberculosis TbRa3 37 Val Ile Asp Ile Ile Gly Thr Ser Pro Thr Ser Trp Glu Gln Ala Ala 1 5 10 15 Ala Glu Ala Val Gln Arg Ala Arg Asp Ser Val Asp Asp Ile Arg Val 20 25 30 Ala Arg Val Ile Glu Gln Asp Met Ala Val Asp Ser Ala Gly Lys Ile 35 40 45 Thr Tyr Arg Ile Lys Leu Glu Val Ser Phe Lys Met Arg Pro Ala Gln 50 55 60 Pro Arg 65 38 1993 DNA Mycobacterium tuberculosis 38 kD 38 tgttcttcga cggcaggctg gtggaggaag ggcccaccga acagctgttc tcctcgccga 60 agcatgcgga aaccgcccga tacgtcgccg gactgtcggg ggacgtcaag gacgccaagc 120 gcggaaattg aagagcacag aaaggtatgg cgtgaaaatt cgtttgcata cgctgttggc 180 cgtgttgacc gctgcgccgc tgctgctagc agcggcgggc tgtggctcga aaccaccgag 240 cggttcgcct gaaacgggcg ccggcgccgg tactgtcgcg actacccccg cgtcgtcgcc 300 ggtgacgttg gcggagaccg gtagcacgct gctctacccg ctgttcaacc tgtggggtcc 360 ggcctttcac gagaggtatc cgaacgtcac gatcaccgct cagggcaccg gttctggtgc 420 cgggatcgcg caggccgccg ccgggacggt caacattggg gcctccgacg cctatctgtc 480 ggaaggtgat atggccgcgc acaaggggct gatgaacatc gcgctagcca tctccgctca 540 gcaggtcaac tacaacctgc ccggagtgag cgagcacctc aagctgaacg gaaaagtcct 600 ggcggccatg taccagggca ccatcaaaac ctgggacgac ccgcagatcg ctgcgctcaa 660 ccccggcgtg aacctgcccg gcaccgcggt agttccgctg caccgctccg acgggtccgg 720 tgacaccttc ttgttcaccc agtacctgtc caagcaagat cccgagggct ggggcaagtc 780 gcccggcttc ggcaccaccg tcgacttccc ggcggtgccg ggtgcgctgg gtgagaacgg 840 caacggcggc atggtgaccg gttgcgccga gacaccgggc tgcgtggcct atatcggcat 900 cagcttcctc gaccaggcca gtcaacgggg actcggcgag gcccaactag gcaatagctc 960 tggcaatttc ttgttgcccg acgcgcaaag cattcaggcc gcggcggctg gcttcgcatc 1020 gaaaaccccg gcgaaccagg cgatttcgat gatcgacggg cccgccccgg acggctaccc 1080 gatcatcaac tacgagtacg ccatcgtcaa caaccggcaa aaggacgccg ccaccgcgca 1140 gaccttgcag gcatttctgc actgggcgat caccgacggc aacaaggcct cgttcctcga 1200 ccaggttcat ttccagccgc tgccgcccgc ggtggtgaag ttgtctgacg cgttgatcgc 1260 gacgatttcc agctagcctc gttgaccacc acgcgacagc aacctccgtc gggccatcgg 1320 gctgctttgc ggagcatgct ggcccgtgcc ggtgaagtcg gccgcgctgg cccggccatc 1380 cggtggttgg gtgggatagg tgcggtgatc ccgctgcttg cgctggtctt ggtgctggtg 1440 gtgctggtca tcgaggcgat gggtgcgatc aggctcaacg ggttgcattt cttcaccgcc 1500 accgaatgga atccaggcaa cacctacggc gaaaccgttg tcaccgacgc gtcgcccatc 1560 cggtcggcgc ctactacggg gcgttgccgc tgatcgtcgg gacgctggcg acctcggcaa 1620 tcgccctgat catcgcggtg ccggtctctg taggagcggc gctggtgatc gtggaacggc 1680 tgccgaaacg gttggccgag gctgtgggaa tagtcctgga attgctcgcc ggaatcccca 1740 gcgtggtcgt cggtttgtgg ggggcaatga cgttcgggcc gttcatcgct catcacatcg 1800 ctccggtgat cgctcacaac gctcccgatg tgccggtgct gaactacttg cgcggcgacc 1860 cgggcaacgg ggagggcatg ttggtgtccg gtctggtgtt ggcggtgatg gtcgttccca 1920 ttatcgccac caccactcat gacctgttcc ggcaggtgcc ggtgttgccc cgggagggcg 1980 cgatcgggaa ttc 1993 39 374 PRT Mycobacterium tuberculosis 38 kD 39 Met Lys Ile Arg Leu His Thr Leu Leu Ala Val Leu Thr Ala Ala Pro 1 5 10 15 Leu Leu Leu Ala Ala Ala Gly Cys Gly Ser Lys Pro Pro Ser Gly Ser 20 25 30 Pro Glu Thr Gly Ala Gly Ala Gly Thr Val Ala Thr Thr Pro Ala Ser 35 40 45 Ser Pro Val Thr Leu Ala Glu Thr Gly Ser Thr Leu Leu Tyr Pro Leu 50 55 60 Phe Asn Leu Trp Gly Pro Ala Phe His Glu Arg Tyr Pro Asn Val Thr 65 70 75 80 Ile Thr Ala Gln Gly Thr Gly Ser Gly Ala Gly Ile Ala Gln Ala Ala 85 90 95 Ala Gly Thr Val Asn Ile Gly Ala Ser Asp Ala Tyr Leu Ser Glu Gly 100 105 110 Asp Met Ala Ala His Lys Gly Leu Met Asn Ile Ala Leu Ala Ile Ser 115 120 125 Ala Gln Gln Val Asn Tyr Asn Leu Pro Gly Val Ser Glu His Leu Lys 130 135 140 Leu Asn Gly Lys Val Leu Ala Ala Met Tyr Gln Gly Thr Ile Lys Thr 145 150 155 160 Trp Asp Asp Pro Gln Ile Ala Ala Leu Asn Pro Gly Val Asn Leu Pro 165 170 175 Gly Thr Ala Val Val Pro Leu His Arg Ser Asp Gly Ser Gly Asp Thr 180 185 190 Phe Leu Phe Thr Gln Tyr Leu Ser Lys Gln Asp Pro Glu Gly Trp Gly 195 200 205 Lys Ser Pro Gly Phe Gly Thr Thr Val Asp Phe Pro Ala Val Pro Gly 210 215 220 Ala Leu Gly Glu Asn Gly Asn Gly Gly Met Val Thr Gly Cys Ala Glu 225 230 235 240 Thr Pro Gly Cys Val Ala Tyr Ile Gly Ile Ser Phe Leu Asp Gln Ala 245 250 255 Ser Gln Arg Gly Leu Gly Glu Ala Gln Leu Gly Asn Ser Ser Gly Asn 260 265 270 Phe Leu Leu Pro Asp Ala Gln Ser Ile Gln Ala Ala Ala Ala Gly Phe 275 280 285 Ala Ser Lys Thr Pro Ala Asn Gln Ala Ile Ser Met Ile Asp Gly Pro 290 295 300 Ala Pro Asp Gly Tyr Pro Ile Ile Asn Tyr Glu Tyr Ala Ile Val Asn 305 310 315 320 Asn Arg Gln Lys Asp Ala Ala Thr Ala Gln Thr Leu Gln Ala Phe Leu 325 330 335 His Trp Ala Ile Thr Asp Gly Asn Lys Ala Ser Phe Leu Asp Gln Val 340 345 350 His Phe Gln Pro Leu Pro Pro Ala Val Val Lys Leu Ser Asp Ala Leu 355 360 365 Ile Ala Thr Ile Ser Ser 370 40 999 DNA Mycobacterium tuberculosis DPEP 40 atgcatcacc atcaccatca catgcatcag gtggacccca acttgacacg tcgcaaggga 60 cgattggcgg cactggctat cgcggcgatg gccagcgcca gcctggtgac cgttgcggtg 120 cccgcgaccg ccaacgccga tccggagcca gcgcccccgg tacccacaac ggccgcctcg 180 ccgccgtcga ccgctgcagc gccacccgca ccggcgacac ctgttgcccc cccaccaccg 240 gccgccgcca acacgccgaa tgcccagccg ggcgatccca acgcagcacc tccgccggcc 300 gacccgaacg caccgccgcc acctgtcatt gccccaaacg caccccaacc tgtccggatc 360 gacaacccgg ttggaggatt cagcttcgcg ctgcctgctg gctgggtgga gtctgacgcc 420 gcccacttcg actacggttc agcactcctc agcaaaacca ccggggaccc gccatttccc 480 ggacagccgc cgccggtggc caatgacacc cgtatcgtgc tcggccggct agaccaaaag 540 ctttacgcca gcgccgaagc caccgactcc aaggccgcgg cccggttggg ctcggacatg 600 ggtgagttct atatgcccta cccgggcacc cggatcaacc aggaaaccgt ctcgctcgac 660 gccaacgggg tgtctggaag cgcgtcgtat tacgaagtca agttcagcga tccgagtaag 720 ccgaacggcc agatctggac gggcgtaatc ggctcgcccg cggcgaacgc accggacgcc 780 gggccccctc agcgctggtt tgtggtatgg ctcgggaccg ccaacaaccc ggtggacaag 840 ggcgcggcca aggcgctggc cgaatcgatc cggcctttgg tcgccccgcc gccggcgccg 900 gcaccggctc ctgcagagcc cgctccggcg ccggcgccgg ccggggaagt cgctcctacc 960 ccgacgacac cgacaccgca gcggacctta ccggcctga 999 41 332 PRT Mycobacterium tuberculosis DPEP 41 Met His His His His His His Met His Gln Val Asp Pro Asn Leu Thr 1 5 10 15 Arg Arg Lys Gly Arg Leu Ala Ala Leu Ala Ile Ala Ala Met Ala Ser 20 25 30 Ala Ser Leu Val Thr Val Ala Val Pro Ala Thr Ala Asn Ala Asp Pro 35 40 45 Glu Pro Ala Pro Pro Val Pro Thr Thr Ala Ala Ser Pro Pro Ser Thr 50 55 60 Ala Ala Ala Pro Pro Ala Pro Ala Thr Pro Val Ala Pro Pro Pro Pro 65 70 75 80 Ala Ala Ala Asn Thr Pro Asn Ala Gln Pro Gly Asp Pro Asn Ala Ala 85 90 95 Pro Pro Pro Ala Asp Pro Asn Ala Pro Pro Pro Pro Val Ile Ala Pro 100 105 110 Asn Ala Pro Gln Pro Val Arg Ile Asp Asn Pro Val Gly Gly Phe Ser 115 120 125 Phe Ala Leu Pro Ala Gly Trp Val Glu Ser Asp Ala Ala His Phe Asp 130 135 140 Tyr Gly Ser Ala Leu Leu Ser Lys Thr Thr Gly Asp Pro Pro Phe Pro 145 150 155 160 Gly Gln Pro Pro Pro Val Ala Asn Asp Thr Arg Ile Val Leu Gly Arg 165 170 175 Leu Asp Gln Lys Leu Tyr Ala Ser Ala Glu Ala Thr Asp Ser Lys Ala 180 185 190 Ala Ala Arg Leu Gly Ser Asp Met Gly Glu Phe Tyr Met Pro Tyr Pro 195 200 205 Gly Thr Arg Ile Asn Gln Glu Thr Val Ser Leu Asp Ala Asn Gly Val 210 215 220 Ser Gly Ser Ala Ser Tyr Tyr Glu Val Lys Phe Ser Asp Pro Ser Lys 225 230 235 240 Pro Asn Gly Gln Ile Trp Thr Gly Val Ile Gly Ser Pro Ala Ala Asn 245 250 255 Ala Pro Asp Ala Gly Pro Pro Gln Arg Trp Phe Val Val Trp Leu Gly 260 265 270 Thr Ala Asn Asn Pro Val Asp Lys Gly Ala Ala Lys Ala Leu Ala Glu 275 280 285 Ser Ile Arg Pro Leu Val Ala Pro Pro Pro Ala Pro Ala Pro Ala Pro 290 295 300 Ala Glu Pro Ala Pro Ala Pro Ala Pro Ala Gly Glu Val Ala Pro Thr 305 310 315 320 Pro Thr Thr Pro Thr Pro Gln Arg Thr Leu Pro Ala 325 330 42 702 DNA Mycobacterium tuberculosis TbH4 42 cggcacgagg atcggtaccc cgcggcatcg gcagctgccg attcgccggg tttccccacc 60 cgaggaaagc cgctaccaga tggcgctgcc gaagtagggc gatccgttcg cgatgccggc 120 atgaacgggc ggcatcaaat tagtgcagga acctttcagt ttagcgacga taatggctat 180 agcactaagg aggatgatcc gatatgacgc agtcgcagac cgtgacggtg gatcagcaag 240 agattttgaa cagggccaac gaggtggagg ccccgatggc ggacccaccg actgatgtcc 300 ccatcacacc gtgcgaactc acggnggnta aaaacgccgc ccaacagntg gtnttgtccg 360 ccgacaacat gcgggaatac ctggcggccg gtgccaaaga gcggcagcgt ctggcgacct 420 cgctgcgcaa cgcggccaag gngtatggcg aggttgatga ggaggctgcg accgcgctgg 480 acaacgacgg cgaaggaact gtgcaggcag aatcggccgg ggccgtcgga ggggacagtt 540 cggccgaact aaccgatacg ccgagggtgg ccacggccgg tgaacccaac ttcatggatc 600 tcaaagaagc ggcaaggaag ctcgaaacgg gcgaccaagg cgcatcgctc gcgcactgng 660 gggatgggtg gaacacttnc accctgacgc tgcaaggcga cg 702 43 286 PRT Mycobacterium tuberculosis TbH4 43 Gly Asp Ser Phe Trp Ala Ala Ala Asp Gln Met Ala Arg Gly Phe Val 1 5 10 15 Leu Gly Ala Thr Ala Gly Arg Thr Thr Leu Thr Gly Glu Gly Leu Gln 20 25 30 His Ala Asp Gly His Ser Leu Leu Leu Asp Ala Thr Asn Pro Ala Val 35 40 45 Val Ala Tyr Asp Pro Ala Phe Ala Tyr Glu Ile Gly Tyr Ile Xaa Glu 50 55 60 Ser Gly Leu Ala Arg Met Cys Gly Glu Asn Pro Glu Asn Ile Phe Phe 65 70 75 80 Tyr Ile Thr Val Tyr Asn Glu Pro Tyr Val Gln Pro Pro Glu Pro Glu 85 90 95 Asn Phe Asp Pro Glu Gly Val Leu Gly Gly Ile Tyr Arg Tyr His Ala 100 105 110 Ala Thr Glu Gln Arg Thr Asn Lys Xaa Gln Ile Leu Ala Ser Gly Val 115 120 125 Ala Met Pro Ala Ala Leu Arg Ala Ala Gln Met Leu Ala Ala Glu Trp 130 135 140 Asp Val Ala Ala Asp Val Trp Ser Val Thr Ser Trp Gly Glu Leu Asn 145 150 155 160 Arg Asp Gly Val Val Ile Glu Thr Glu Lys Leu Arg His Pro Asp Arg 165 170 175 Pro Ala Gly Val Pro Tyr Val Thr Arg Ala Leu Glu Asn Ala Arg Gly 180 185 190 Pro Val Ile Ala Val Ser Asp Trp Met Arg Ala Val Pro Glu Gln Ile 195 200 205 Arg Pro Trp Val Pro Gly Thr Tyr Leu Thr Leu Gly Thr Asp Gly Phe 210 215 220 Gly Phe Ser Asp Thr Arg Pro Ala Gly Arg Arg Tyr Phe Asn Thr Asp 225 230 235 240 Ala Glu Ser Gln Val Gly Arg Gly Phe Gly Arg Gly Trp Pro Gly Arg 245 250 255 Arg Val Asn Ile Asp Pro Phe Gly Ala Gly Arg Gly Pro Pro Ala Gln 260 265 270 Leu Pro Gly Phe Asp Glu Gly Gly Gly Leu Arg Pro Xaa Lys 275 280 285 44 339 DNA Mycobacterium tuberculosis DPPD genomic DNA 44 atgaagttga agtttgctcg cctgagtact gcgatactgg gttgtgcagc ggcgcttgtg 60 tttcctgcct cggttgccag cgcagatcca cctgacccgc atcagccgga catgacgaaa 120 ggctattgcc cgggtggccg atggggtttt ggcgacttgg ccgtgtgcga cggcgagaag 180 taccccgacg gctcgttttg gcaccagtgg atgcaaacgt ggtttaccgg cccacagttt 240 tacttcgatt gtgtcagcgg cggtgagccc ctccccggcc cgccgccacc gggtggttgc 300 ggtggggcaa ttccgtccga gcagcccaac gctccctga 339 45 112 PRT Mycobacterium tuberculosis DPPD 45 Met Lys Leu Lys Phe Ala Arg Leu Ser Thr Ala Ile Leu Gly Cys Ala 1 5 10 15 Ala Ala Leu Val Phe Pro Ala Ser Val Ala Ser Ala Asp Pro Pro Asp 20 25 30 Pro His Gln Pro Asp Met Thr Lys Gly Tyr Cys Pro Gly Gly Arg Trp 35 40 45 Gly Phe Gly Asp Leu Ala Val Cys Asp Gly Glu Lys Tyr Pro Asp Gly 50 55 60 Ser Phe Trp His Gln Trp Met Gln Thr Trp Phe Thr Gly Pro Gln Phe 65 70 75 80 Tyr Phe Asp Cys Val Ser Gly Gly Glu Pro Leu Pro Gly Pro Pro Pro 85 90 95 Pro Gly Gly Cys Gly Gly Ala Ile Pro Ser Glu Gln Pro Asn Ala Pro 100 105 110 46 921 DNA Artificial Sequence Description of Artificial Sequencetri-fusion protein DPV-MTI-MSL (designated MTb31F) cDNA 46 cat atg cat cac cat cac cat cac gat ccc gtg gac gcg gtc att aac 48 His Met His His His His His His Asp Pro Val Asp Ala Val Ile Asn 1 5 10 15 acc acc tgc aat tac ggg cag gta gta gct gcg ctc aac gcg acg gat 96 Thr Thr Cys Asn Tyr Gly Gln Val Val Ala Ala Leu Asn Ala Thr Asp 20 25 30 ccg ggg gct gcc gca cag ttc aac gcc tca ccg gtg gcg cag tcc tat 144 Pro Gly Ala Ala Ala Gln Phe Asn Ala Ser Pro Val Ala Gln Ser Tyr 35 40 45 ttg cgc aat ttc ctc gcc gca ccg cca cct cag cgc gct gcc atg gcc 192 Leu Arg Asn Phe Leu Ala Ala Pro Pro Pro Gln Arg Ala Ala Met Ala 50 55 60 gcg caa ttg caa gct gtg ccg ggg gcg gca cag tac atc ggc ctt gtc 240 Ala Gln Leu Gln Ala Val Pro Gly Ala Ala Gln Tyr Ile Gly Leu Val 65 70 75 80 gag tcg gtt gcc ggc tcc tgc aac aac tat gag ctc atg acg att aat 288 Glu Ser Val Ala Gly Ser Cys Asn Asn Tyr Glu Leu Met Thr Ile Asn 85 90 95 tac cag ttc ggg gac gtc gac gct cat ggc gcc atg atc cgc gct cag 336 Tyr Gln Phe Gly Asp Val Asp Ala His Gly Ala Met Ile Arg Ala Gln 100 105 110 gcg gcg tcg ctt gag gcg gag cat cag gcc atc gtt cgt gat gtg ttg 384 Ala Ala Ser Leu Glu Ala Glu His Gln Ala Ile Val Arg Asp Val Leu 115 120 125 gcc gcg ggt gac ttt tgg ggc ggc gcc ggt tcg gtg gct tgc cag gag 432 Ala Ala Gly Asp Phe Trp Gly Gly Ala Gly Ser Val Ala Cys Gln Glu 130 135 140 ttc att acc cag ttg ggc cgt aac ttc cag gtg atc tac gag cag gcc 480 Phe Ile Thr Gln Leu Gly Arg Asn Phe Gln Val Ile Tyr Glu Gln Ala 145 150 155 160 aac gcc cac ggg cag aag gtg cag gct gcc ggc aac aac atg gcg caa 528 Asn Ala His Gly Gln Lys Val Gln Ala Ala Gly Asn Asn Met Ala Gln 165 170 175 acc gac agc gcc gtc ggc tcc agc tgg gcc act agt atg agc ctt ttg 576 Thr Asp Ser Ala Val Gly Ser Ser Trp Ala Thr Ser Met Ser Leu Leu 180 185 190 gat gct cat atc cca cag ttg gtg gcc tcc cag tcg gcg ttt gcc gcc 624 Asp Ala His Ile Pro Gln Leu Val Ala Ser Gln Ser Ala Phe Ala Ala 195 200 205 aag gcg ggg ctg atg cgg cac acg atc ggt cag gcc gag cag gcg gcg 672 Lys Ala Gly Leu Met Arg His Thr Ile Gly Gln Ala Glu Gln Ala Ala 210 215 220 atg tcg gct cag gcg ttt cac cag ggg gag tcg tcg gcg gcg ttt cag 720 Met Ser Ala Gln Ala Phe His Gln Gly Glu Ser Ser Ala Ala Phe Gln 225 230 235 240 gcc gcc cat gcc cgg ttt gtg gcg gcg gcc gcc aaa gtc aac acc ttg 768 Ala Ala His Ala Arg Phe Val Ala Ala Ala Ala Lys Val Asn Thr Leu 245 250 255 ttg gat gtc gcg cag gcg aat ctg ggt gag gcc gcc ggt acc tat gtg 816 Leu Asp Val Ala Gln Ala Asn Leu Gly Glu Ala Ala Gly Thr Tyr Val 260 265 270 gcc gcc gat gct gcg gcc gcg tcg acc tat acc ggg ttc gat atc cat 864 Ala Ala Asp Ala Ala Ala Ala Ser Thr Tyr Thr Gly Phe Asp Ile His 275 280 285 cac act ggc ggc cgc tcg agc aga tcc ggc tgc taa caaagcccga 910 His Thr Gly Gly Arg Ser Ser Arg Ser Gly Cys 290 295 aaggaagctg a 921 47 299 PRT Artificial Sequence Description of Artificial Sequencetri-fusion protein DPV-MTI-MSL (designated MTb31F) cDNA 47 His Met His His His His His His Asp Pro Val Asp Ala Val Ile Asn 1 5 10 15 Thr Thr Cys Asn Tyr Gly Gln Val Val Ala Ala Leu Asn Ala Thr Asp 20 25 30 Pro Gly Ala Ala Ala Gln Phe Asn Ala Ser Pro Val Ala Gln Ser Tyr 35 40 45 Leu Arg Asn Phe Leu Ala Ala Pro Pro Pro Gln Arg Ala Ala Met Ala 50 55 60 Ala Gln Leu Gln Ala Val Pro Gly Ala Ala Gln Tyr Ile Gly Leu Val 65 70 75 80 Glu Ser Val Ala Gly Ser Cys Asn Asn Tyr Glu Leu Met Thr Ile Asn 85 90 95 Tyr Gln Phe Gly Asp Val Asp Ala His Gly Ala Met Ile Arg Ala Gln 100 105 110 Ala Ala Ser Leu Glu Ala Glu His Gln Ala Ile Val Arg Asp Val Leu 115 120 125 Ala Ala Gly Asp Phe Trp Gly Gly Ala Gly Ser Val Ala Cys Gln Glu 130 135 140 Phe Ile Thr Gln Leu Gly Arg Asn Phe Gln Val Ile Tyr Glu Gln Ala 145 150 155 160 Asn Ala His Gly Gln Lys Val Gln Ala Ala Gly Asn Asn Met Ala Gln 165 170 175 Thr Asp Ser Ala Val Gly Ser Ser Trp Ala Thr Ser Met Ser Leu Leu 180 185 190 Asp Ala His Ile Pro Gln Leu Val Ala Ser Gln Ser Ala Phe Ala Ala 195 200 205 Lys Ala Gly Leu Met Arg His Thr Ile Gly Gln Ala Glu Gln Ala Ala 210 215 220 Met Ser Ala Gln Ala Phe His Gln Gly Glu Ser Ser Ala Ala Phe Gln 225 230 235 240 Ala Ala His Ala Arg Phe Val Ala Ala Ala Ala Lys Val Asn Thr Leu 245 250 255 Leu Asp Val Ala Gln Ala Asn Leu Gly Glu Ala Ala Gly Thr Tyr Val 260 265 270 Ala Ala Asp Ala Ala Ala Ala Ser Thr Tyr Thr Gly Phe Asp Ile His 275 280 285 His Thr Gly Gly Arg Ser Ser Arg Ser Gly Cys 290 295 48 2168 DNA Artificial Sequence Description of Artificial Sequencetetra-fusion protein DPV-MTI-MSL-MTCC#2 (designated MTb71F) 48 cat atg cat cac cat cac cat cac gat ccc gtg gac gcg gtc att aac 48 His Met His His His His His His Asp Pro Val Asp Ala Val Ile Asn 1 5 10 15 acc acc tgc aat tac ggg cag gta gta gct gcg ctc aac gcg acg gat 96 Thr Thr Cys Asn Tyr Gly Gln Val Val Ala Ala Leu Asn Ala Thr Asp 20 25 30 ccg ggg gct gcc gca cag ttc aac gcc tca ccg gtg gcg cag tcc tat 144 Pro Gly Ala Ala Ala Gln Phe Asn Ala Ser Pro Val Ala Gln Ser Tyr 35 40 45 ttg cgc aat ttc ctc gcc gca ccg cca cct cag cgc gct gcc atg gcc 192 Leu Arg Asn Phe Leu Ala Ala Pro Pro Pro Gln Arg Ala Ala Met Ala 50 55 60 gcg caa ttg caa gct gtg ccg ggg gcg gca cag tac atc ggc ctt gtc 240 Ala Gln Leu Gln Ala Val Pro Gly Ala Ala Gln Tyr Ile Gly Leu Val 65 70 75 80 gag tcg gtt gcc ggc tcc tgc aac aac tat gag ctc atg acg att aat 288 Glu Ser Val Ala Gly Ser Cys Asn Asn Tyr Glu Leu Met Thr Ile Asn 85 90 95 tac cag ttc ggg gac gtc gac gct cat ggc gcc atg atc cgc gct cag 336 Tyr Gln Phe Gly Asp Val Asp Ala His Gly Ala Met Ile Arg Ala Gln 100 105 110 gcg gcg tcg ctt gag gcg gag cat cag gcc atc gtt cgt gat gtg ttg 384 Ala Ala Ser Leu Glu Ala Glu His Gln Ala Ile Val Arg Asp Val Leu 115 120 125 gcc gcg ggt gac ttt tgg ggc ggc gcc ggt tcg gtg gct tgc cag gag 432 Ala Ala Gly Asp Phe Trp Gly Gly Ala Gly Ser Val Ala Cys Gln Glu 130 135 140 ttc att acc cag ttg ggc cgt aac ttc cag gtg atc tac gag cag gcc 480 Phe Ile Thr Gln Leu Gly Arg Asn Phe Gln Val Ile Tyr Glu Gln Ala 145 150 155 160 aac gcc cac ggg cag aag gtg cag gct gcc ggc aac aac atg gcg caa 528 Asn Ala His Gly Gln Lys Val Gln Ala Ala Gly Asn Asn Met Ala Gln 165 170 175 acc gac agc gcc gtc ggc tcc agc tgg gcc act agt atg agc ctt ttg 576 Thr Asp Ser Ala Val Gly Ser Ser Trp Ala Thr Ser Met Ser Leu Leu 180 185 190 gat gct cat atc cca cag ttg gtg gcc tcc cag tcg gcg ttt gcc gcc 624 Asp Ala His Ile Pro Gln Leu Val Ala Ser Gln Ser Ala Phe Ala Ala 195 200 205 aag gcg ggg ctg atg cgg cac acg atc ggt cag gcc gag cag gcg gcg 672 Lys Ala Gly Leu Met Arg His Thr Ile Gly Gln Ala Glu Gln Ala Ala 210 215 220 atg tcg gct cag gcg ttt cac cag ggg gag tcg tcg gcg gcg ttt cag 720 Met Ser Ala Gln Ala Phe His Gln Gly Glu Ser Ser Ala Ala Phe Gln 225 230 235 240 gcc gcc cat gcc cgg ttt gtg gcg gcg gcc gcc aaa gtc aac acc ttg 768 Ala Ala His Ala Arg Phe Val Ala Ala Ala Ala Lys Val Asn Thr Leu 245 250 255 ttg gat gtc gcg cag gcg aat ctg ggt gag gcc gcc ggt acc tat gtg 816 Leu Asp Val Ala Gln Ala Asn Leu Gly Glu Ala Ala Gly Thr Tyr Val 260 265 270 gcc gcc gat gct gcg gcc gcg tcg acc tat acc ggg ttc gat atc atg 864 Ala Ala Asp Ala Ala Ala Ala Ser Thr Tyr Thr Gly Phe Asp Ile Met 275 280 285 gat ttc ggg ctt tta cct ccg gaa gtg aat tca agc cga atg tat tcc 912 Asp Phe Gly Leu Leu Pro Pro Glu Val Asn Ser Ser Arg Met Tyr Ser 290 295 300 ggt ccg ggg ccg gag tcg atg cta gcc gcc gcg gcc gcc tgg gac ggt 960 Gly Pro Gly Pro Glu Ser Met Leu Ala Ala Ala Ala Ala Trp Asp Gly 305 310 315 320 gtg gcc gcg gag ttg act tcc gcc gcg gtc tcg tat gga tcg gtg gtg 1008 Val Ala Ala Glu Leu Thr Ser Ala Ala Val Ser Tyr Gly Ser Val Val 325 330 335 tcg acg ctg atc gtt gag ccg tgg atg ggg ccg gcg gcg gcc gcg atg 1056 Ser Thr Leu Ile Val Glu Pro Trp Met Gly Pro Ala Ala Ala Ala Met 340 345 350 gcg gcc gcg gca acg ccg tat gtg ggg tgg ctg gcc gcc acg gcg gcg 1104 Ala Ala Ala Ala Thr Pro Tyr Val Gly Trp Leu Ala Ala Thr Ala Ala 355 360 365 ctg gcg aag gag acg gcc aca cag gcg agg gca gcg gcg gaa gcg ttt 1152 Leu Ala Lys Glu Thr Ala Thr Gln Ala Arg Ala Ala Ala Glu Ala Phe 370 375 380 ggg acg gcg ttc gcg atg acg gtg cca cca tcc ctc gtc gcg gcc aac 1200 Gly Thr Ala Phe Ala Met Thr Val Pro Pro Ser Leu Val Ala Ala Asn 385 390 395 400 cgc agc cgg ttg atg tcg ctg gtc gcg gcg aac att ctg ggg caa aac 1248 Arg Ser Arg Leu Met Ser Leu Val Ala Ala Asn Ile Leu Gly Gln Asn 405 410 415 agt gcg gcg atc gcg gct acc cag gcc gag tat gcc gaa atg tgg gcc 1296 Ser Ala Ala Ile Ala Ala Thr Gln Ala Glu Tyr Ala Glu Met Trp Ala 420 425 430 caa gac gct gcc gtg atg tac agc tat gag ggg gca tct gcg gcc gcg 1344 Gln Asp Ala Ala Val Met Tyr Ser Tyr Glu Gly Ala Ser Ala Ala Ala 435 440 445 tcg gcg ttg ccg ccg ttc act cca ccc gtg caa ggc acc ggc ccg gcc 1392 Ser Ala Leu Pro Pro Phe Thr Pro Pro Val Gln Gly Thr Gly Pro Ala 450 455 460 ggg ccc gcg gcc gca gcc gcg gcg acc caa gcc gcc ggt gcg ggc gcc 1440 Gly Pro Ala Ala Ala Ala Ala Ala Thr Gln Ala Ala Gly Ala Gly Ala 465 470 475 480 gtt gcg gat gca cag gcg aca ctg gcc cag ctg ccc ccg ggg atc ctg 1488 Val Ala Asp Ala Gln Ala Thr Leu Ala Gln Leu Pro Pro Gly Ile Leu 485 490 495 agc gac att ctg tcc gca ttg gcc gcc aac gct gat ccg ctg aca tcg 1536 Ser Asp Ile Leu Ser Ala Leu Ala Ala Asn Ala Asp Pro Leu Thr Ser 500 505 510 gga ctg ttg ggg atc gcg tcg acc ctc aac ccg caa gtc gga tcc gct 1584 Gly Leu Leu Gly Ile Ala Ser Thr Leu Asn Pro Gln Val Gly Ser Ala 515 520 525 cag ccg ata gtg atc ccc acc ccg ata ggg gaa ttg gac gtg atc gcg 1632 Gln Pro Ile Val Ile Pro Thr Pro Ile Gly Glu Leu Asp Val Ile Ala 530 535 540 ctc tac att gca tcc atc gcg acc ggc agc att gcg ctc gcg atc acg 1680 Leu Tyr Ile Ala Ser Ile Ala Thr Gly Ser Ile Ala Leu Ala Ile Thr 545 550 555 560 aac acg gcc aga ccc tgg cac atc ggc cta tac ggg aac gcc ggc ggg 1728 Asn Thr Ala Arg Pro Trp His Ile Gly Leu Tyr Gly Asn Ala Gly Gly 565 570 575 ctg gga ccg acg cag ggc cat cca ctg agt tcg gcg acc gac gag ccg 1776 Leu Gly Pro Thr Gln Gly His Pro Leu Ser Ser Ala Thr Asp Glu Pro 580 585 590 gag ccg cac tgg ggc ccc ttc ggg ggc gcg gcg ccg gtg tcc gcg ggc 1824 Glu Pro His Trp Gly Pro Phe Gly Gly Ala Ala Pro Val Ser Ala Gly 595 600 605 gtc ggc cac gca gca tta gtc gga gcg ttg tcg gtg ccg cac agc tgg 1872 Val Gly His Ala Ala Leu Val Gly Ala Leu Ser Val Pro His Ser Trp 610 615 620 acc acg gcc gcc ccg gag atc cag ctc gcc gtt cag gca aca ccc acc 1920 Thr Thr Ala Ala Pro Glu Ile Gln Leu Ala Val Gln Ala Thr Pro Thr 625 630 635 640 ttc agc tcc agc gcc ggc gcc gac ccg acg gcc cta aac ggg atg ccg 1968 Phe Ser Ser Ser Ala Gly Ala Asp Pro Thr Ala Leu Asn Gly Met Pro 645 650 655 gca ggc ctg ctc agc ggg atg gct ttg gcg agc ctg gcc gca cgc ggc 2016 Ala Gly Leu Leu Ser Gly Met Ala Leu Ala Ser Leu Ala Ala Arg Gly 660 665 670 acg acg ggc ggt ggc ggc acc cgt agc ggc acc agc act gac ggc caa 2064 Thr Thr Gly Gly Gly Gly Thr Arg Ser Gly Thr Ser Thr Asp Gly Gln 675 680 685 gag gac ggc cgc aaa ccc ccg gta gtt gtg att aga gag cag ccg ccg 2112 Glu Asp Gly Arg Lys Pro Pro Val Val Val Ile Arg Glu Gln Pro Pro 690 695 700 ccc gga aac ccc ccg cgg taa gatttctaaa tccatcacac tggcggccgc 2163 Pro Gly Asn Pro Pro Arg 705 710 tcgag 2168 49 710 PRT Artificial Sequence Description of Artificial Sequencetetra-fusion protein DPV-MTI-MSL-MTCC#2 (designated MTb71F) 49 His Met His His His His His His Asp Pro Val Asp Ala Val Ile Asn 1 5 10 15 Thr Thr Cys Asn Tyr Gly Gln Val Val Ala Ala Leu Asn Ala Thr Asp 20 25 30 Pro Gly Ala Ala Ala Gln Phe Asn Ala Ser Pro Val Ala Gln Ser Tyr 35 40 45 Leu Arg Asn Phe Leu Ala Ala Pro Pro Pro Gln Arg Ala Ala Met Ala 50 55 60 Ala Gln Leu Gln Ala Val Pro Gly Ala Ala Gln Tyr Ile Gly Leu Val 65 70 75 80 Glu Ser Val Ala Gly Ser Cys Asn Asn Tyr Glu Leu Met Thr Ile Asn 85 90 95 Tyr Gln Phe Gly Asp Val Asp Ala His Gly Ala Met Ile Arg Ala Gln 100 105 110 Ala Ala Ser Leu Glu Ala Glu His Gln Ala Ile Val Arg Asp Val Leu 115 120 125 Ala Ala Gly Asp Phe Trp Gly Gly Ala Gly Ser Val Ala Cys Gln Glu 130 135 140 Phe Ile Thr Gln Leu Gly Arg Asn Phe Gln Val Ile Tyr Glu Gln Ala 145 150 155 160 Asn Ala His Gly Gln Lys Val Gln Ala Ala Gly Asn Asn Met Ala Gln 165 170 175 Thr Asp Ser Ala Val Gly Ser Ser Trp Ala Thr Ser Met Ser Leu Leu 180 185 190 Asp Ala His Ile Pro Gln Leu Val Ala Ser Gln Ser Ala Phe Ala Ala 195 200 205 Lys Ala Gly Leu Met Arg His Thr Ile Gly Gln Ala Glu Gln Ala Ala 210 215 220 Met Ser Ala Gln Ala Phe His Gln Gly Glu Ser Ser Ala Ala Phe Gln 225 230 235 240 Ala Ala His Ala Arg Phe Val Ala Ala Ala Ala Lys Val Asn Thr Leu 245 250 255 Leu Asp Val Ala Gln Ala Asn Leu Gly Glu Ala Ala Gly Thr Tyr Val 260 265 270 Ala Ala Asp Ala Ala Ala Ala Ser Thr Tyr Thr Gly Phe Asp Ile Met 275 280 285 Asp Phe Gly Leu Leu Pro Pro Glu Val Asn Ser Ser Arg Met Tyr Ser 290 295 300 Gly Pro Gly Pro Glu Ser Met Leu Ala Ala Ala Ala Ala Trp Asp Gly 305 310 315 320 Val Ala Ala Glu Leu Thr Ser Ala Ala Val Ser Tyr Gly Ser Val Val 325 330 335 Ser Thr Leu Ile Val Glu Pro Trp Met Gly Pro Ala Ala Ala Ala Met 340 345 350 Ala Ala Ala Ala Thr Pro Tyr Val Gly Trp Leu Ala Ala Thr Ala Ala 355 360 365 Leu Ala Lys Glu Thr Ala Thr Gln Ala Arg Ala Ala Ala Glu Ala Phe 370 375 380 Gly Thr Ala Phe Ala Met Thr Val Pro Pro Ser Leu Val Ala Ala Asn 385 390 395 400 Arg Ser Arg Leu Met Ser Leu Val Ala Ala Asn Ile Leu Gly Gln Asn 405 410 415 Ser Ala Ala Ile Ala Ala Thr Gln Ala Glu Tyr Ala Glu Met Trp Ala 420 425 430 Gln Asp Ala Ala Val Met Tyr Ser Tyr Glu Gly Ala Ser Ala Ala Ala 435 440 445 Ser Ala Leu Pro Pro Phe Thr Pro Pro Val Gln Gly Thr Gly Pro Ala 450 455 460 Gly Pro Ala Ala Ala Ala Ala Ala Thr Gln Ala Ala Gly Ala Gly Ala 465 470 475 480 Val Ala Asp Ala Gln Ala Thr Leu Ala Gln Leu Pro Pro Gly Ile Leu 485 490 495 Ser Asp Ile Leu Ser Ala Leu Ala Ala Asn Ala Asp Pro Leu Thr Ser 500 505 510 Gly Leu Leu Gly Ile Ala Ser Thr Leu Asn Pro Gln Val Gly Ser Ala 515 520 525 Gln Pro Ile Val Ile Pro Thr Pro Ile Gly Glu Leu Asp Val Ile Ala 530 535 540 Leu Tyr Ile Ala Ser Ile Ala Thr Gly Ser Ile Ala Leu Ala Ile Thr 545 550 555 560 Asn Thr Ala Arg Pro Trp His Ile Gly Leu Tyr Gly Asn Ala Gly Gly 565 570 575 Leu Gly Pro Thr Gln Gly His Pro Leu Ser Ser Ala Thr Asp Glu Pro 580 585 590 Glu Pro His Trp Gly Pro Phe Gly Gly Ala Ala Pro Val Ser Ala Gly 595 600 605 Val Gly His Ala Ala Leu Val Gly Ala Leu Ser Val Pro His Ser Trp 610 615 620 Thr Thr Ala Ala Pro Glu Ile Gln Leu Ala Val Gln Ala Thr Pro Thr 625 630 635 640 Phe Ser Ser Ser Ala Gly Ala Asp Pro Thr Ala Leu Asn Gly Met Pro 645 650 655 Ala Gly Leu Leu Ser Gly Met Ala Leu Ala Ser Leu Ala Ala Arg Gly 660 665 670 Thr Thr Gly Gly Gly Gly Thr Arg Ser Gly Thr Ser Thr Asp Gly Gln 675 680 685 Glu Asp Gly Arg Lys Pro Pro Val Val Val Ile Arg Glu Gln Pro Pro 690 695 700 Pro Gly Asn Pro Pro Arg 705 710 50 588 DNA Mycobacterium tuberculosis Ra35 N-terminus of MTB32A (Ra35FL) 50 gccccgccgg ccttgtcgca ggaccggttc gccgacttcc ccgcgctgcc cctcgacccg 60 tccgcgatgg tcgcccaagt ggggccacag gtggtcaaca tcaacaccaa actgggctac 120 aacaacgccg tgggcgccgg gaccggcatc gtcatcgatc ccaacggtgt cgtgctgacc 180 aacaaccacg tgatcgcggg cgccaccgac atcaatgcgt tcagcgtcgg ctccggccaa 240 acctacggcg tcgatgtggt cgggtatgac cgcacccagg atgtcgcggt gctgcagctg 300 cgcggtgccg gtggcctgcc gtcggcggcg atcggtggcg gcgtcgcggt tggtgagccc 360 gtcgtcgcga tgggcaacag cggtgggcag ggcggaacgc cccgtgcggt gcctggcagg 420 gtggtcgcgc tcggccaaac cgtgcaggcg tcggattcgc tgaccggtgc cgaagagaca 480 ttgaacgggt tgatccagtt cgatgccgcg atccagcccg gtgaggcggg cgggcccgtc 540 gtcaacggcc taggacaggt ggtcggtatg aacacggccg cgtcctag 588 

What is claimed is
 1. A composition comprising a MTB39 antigen (SEQ ID NO: 12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex.
 2. The composition of claim 1, comprising a MTB39 antigen (SEQ ID NO: 12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 3. The composition of claim 2, further comprising a polypeptide comprising at least about 132 amino acids from the C-terminus of MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 4. The composition of claims 1, 2, or 3, wherein the antigens are covalently linked, thereby forming a fusion polypeptide.
 5. The composition of claim 4, wherein the fusion polypeptide has the amino acid sequence of MTB59F (SEQ ID NO:20).
 6. The composition of claim 4, wherein the fusion polypeptide has the amino acid sequence of MTB72F (SEQ ID NO:16).
 7. The composition of claim 4, wherein the fusion polypeptide has the amino acid sequence of MTB72FMutSA (SEQ ID NO:18).
 8. The composition of claim 6 or 7, further comprising BCG.
 9. The composition of claim 6 or 7, further comprising at least one additional antigen from a Mycobacterium species of the tuberculosis complex, wherein the antigen is selected from the group consisting of MTB8.4 antigen (SEQ ID NO:22), MTB9.8 antigen (SEQ ID NO:24), MTB9.9 antigen (SEQ ID NO:27), MTB40 antigen (SEQ ID NO:29), MTB41 antigen (SEQ ID NO:31), 38-1 (SEQ ID NO:35), TbRa3 (SEQ ID NO:37), 38 kD (SEQ ID NO:39), DPEP (SEQ ID NO:41), TbH4 (SEQ ID NO:43), DPPD(SEQ ID NO:45), MTB82, Erd14, ESAT-6 antigen (SEQ ID NO:33), MTB85 complex antigen, or α-crystalline antigen, or an immunogenic fragment thereof.
 10. The composition of claim 6 or 7, further comprising an adjuvant.
 11. The composition of claim 4, wherein the antigens are covalently linked via a chemical linker.
 12. The composition of claim 11, wherein the chemical linker is an amino acid linker.
 13. The composition of claim 1, further comprising at least one additional antigen from a Mycobacterium species of the tuberculosis complex, wherein the antigen is selected from the group consisting ofMTB8.4 antigen (SEQ ID NO:22), MTB9.8 antigen (SEQ ID NO:24), MTB9.9 antigen (SEQ ID NO:27), MTB40 antigen (SEQ ID NO:29), MTB41 antigen (SEQ ID NO:31), 38-1 (SEQ ID NO:35), TbRa3 (SEQ ID NO:37), 38 kD (SEQ ID NO:39), DPEP (SEQ ID NO:41), TbH4 (SEQ ID NO:43), DPPD(SEQ ID NO:45), MTB82, Erd14, ESAT-6 antigen (SEQ ID NO:33), MTB85 complex antigen, or α-crystalline antigen, or an immunogenic fragment thereof.
 14. The composition of claim 1, further comprising an adjuvant.
 15. The composition of claim 14, wherein the adjuvant comprises QS21 and MPL.
 16. The composition of claim 14, wherein the adjuvant is selected from the group consisting of AS2, ENHANZYN, MPL, 3D-MPL, IFA, QS21, CWS, TDM, AGP, CPG, Leif, saponin, and saponin mimetics.
 17. The composition of claim 1, further comprising BCG or pVac.
 18. The composition of claim 1, further comprising an NS1 antigen or an immunogenic fragment thereof.
 19. The composition of claim 1, wherein the Mycobacterium species is Mycobacterium tuberculosis.
 20. An expression cassette comprising a nucleic acid encoding a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a nucleic acid encoding a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex.
 21. The expression cassette of claim 20, comprising a nucleic acid encoding a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a nucleic acid encoding a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 22. The expression cassette of claim 21, further comprising a nucleic acid encoding a polypeptide comprising at least 132 amino acids of the C-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 23. The expression cassette of claim 20, wherein the nucleic acid encodes a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof and a nucleic acid encoding a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof.
 24. The expression cassette of claim 23, wherein the nucleic acid encodes a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof, and a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4).
 25. The expression cassette of claim 24, wherein the fusion polypeptide further comprises a polypeptide comprising at least 132 amino acids of the C-terminus of a MTB32A antigen (SEQ ID NO:2 or 4).
 26. The expression cassette of claim 24, wherein the nucleic acid encodes a fusion polypeptide having the amino acid sequence of MTB59F (SEQ ID NO:20).
 27. The expression cassette of claim 26, wherein the nucleic acid has the sequence of the nucleic acid encoding MTB59F (SEQ ID NO:19).
 28. The expression cassette of claim 25, wherein the nucleic acid encodes a fusion polypeptide having the amino acid sequence of MTB72F (SEQ ID NO:16).
 29. The expression cassette of claim 28, wherein the nucleic acid has the sequence of the nucleic acid encoding MTB72F (SEQ ID NO:15).
 30. The expression cassette of claim 28, wherein the nucleic acid has the sequence of the nucleic acid encoding MTB72FMutSA (SEQ ID NO:18).
 31. The expression cassette of claim 29or 30, further comprising a nucleic acid encoding at least one additional antigen from a Mycobacterium species of the tuberculosis complex, wherein the antigen is selected from the group consisting ofMTB8.4 antigen (SEQ ID NO:22), MTB9.8 antigen (SEQ ID NO:24), MTB9.9 antigen (SEQ ID NO:27), MTB40 antigen (SEQ ID NO:29), MTB41 antigen (SEQ ID NO:31), 38-1 (SEQ ID NO:35), TbRa3 (SEQ ID NO:37), 38 kD (SEQ ID NO:39), DPEP (SEQ ID NO:41), TbH4 (SEQ ID NO:43), DPPD(SEQ ID NO:45), MTB82, Erd14, ESAT-6 antigen (SEQ ID NO:33), MTB85 complex antigen, or α-crystalline antigen, or an immunogenic fragment thereof.
 32. The expression cassette of claim 20, further comprising a nucleic acid encoding at least one additional antigen from a Mycobacterium species of the tuberculosis complex, wherein the antigen is selected from the group consisting ofMTB8.4 antigen (SEQ ID NO:22), MTB9.8 antigen (SEQ ID NO:24), MTB9.9 antigen (SEQ ID NO:27), MTB40 antigen (SEQ ID NO:29), MTB41 antigen (SEQ ID NO:31), 38-1 (SEQ ID NO:35), TbRa3 (SEQ ID NO:37), 38 kD (SEQ ID NO:39), DPEP (SEQ ID NO:41), TbH4 (SEQ ID NO:43), DPPD(SEQ ID NO:45), MTB82, Erd14, ESAT-6 antigen (SEQ ID NO:33), MTB85 complex antigen, or α-crystalline antigen, or an immunogenic fragment thereof.
 33. The expression cassette of claim 20, further comprising a nucleic acid encoding an NS 1 antigen.
 34. The expression cassette of claim 20, wherein the Mycobacterium species is Mycobacterium tuberculosis.
 35. A method for eliciting an immune response in a mammal, the method comprising the step of administering to the mammal an immunologically effective amount of a pharmaceutical composition comprising a MTB39 antigen (SEQ ID NO: 12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex.
 36. The method of claim 35, wherein the mammal has been immunized with BCG.
 37. The method of claim 35, wherein the mammal is a human.
 38. The method of claim 35, wherein the composition is administered prophylactically.
 39. The method of claim 35, comprising a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 40. The method of claim 39, further comprising a polypeptide comprising at least about 132 amino acids from the C-terminus of MTB32A antigen (SEQ ID NO: 2 or 4) from a Mycobacterium species of the tuberculosis complex.
 41. The method of claim 35 or 39, wherein the antigens are covalently linked, thereby forming a fusion protein.
 42. The method of claim 41, wherein the fusion polypeptide has the amino acid sequence of MTB59F (SEQ ID NO:20).
 43. The method of claim 40, wherein the antigens are covalently linked, thereby forming a fusion protein.
 44. The method of claim 43, wherein the fusion polypeptide has the amino acid sequence of MTB72F (SEQ ID NO:16).
 45. The method of claim 43, wherein the fusion polypeptide has the amino acid sequence of MTB72FMutSA (SEQ ID NO:18).
 46. The method of claim 35, wherein the pharmaceutical composition further comprises an adjuvant.
 47. The method of claim 46, wherein the adjuvant comprises QS21 and MPL.
 48. The method of claim 46, wherein the adjuvant is selected from the group consisting of AS2, ENHANZYN, MPL, 3D-MPL, IFA, QS21, CWS, TDM, AGP, CPG, Leif, saponin, and saponin mimetics.
 49. A method for eliciting an immune response in a mammal, the method comprising the step of administering to the mammal an immunologically effective amount of an expression cassette comprising a nucleic acid encoding a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex, and a nucleic acid encoding a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof from a Mycobacterium species of the tuberculosis complex.
 50. The method of claim 49, wherein the mammal has been immunized with BCG.
 51. The method of claim 49, wherein the mammal is a human.
 52. The method of claim 49, wherein the composition is administered prophylactically.
 53. The method of claim 49, wherein the nucleic acid encodes a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof, and a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4).
 54. The method of claim 53, further comprising a nucleic acid encoding a polypeptide comprising at least 132 amino acids of the C-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex.
 55. The method of claim 49, wherein the nucleic acid encodes a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO: 12 or 14) or an immunogenic fragment thereof and a nucleic acid encoding a MTB32A antigen (SEQ ID NO:2 or 4) or an immunogenic fragment thereof.
 56. The method of claim 55, wherein the nucleic acid encodes a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO:12 or 14) or an immunogenic fragment thereof, and a polypeptide comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO: 2 or 4).
 57. The method of claim 56, wherein the fusion polypeptide further comprises a polypeptide comprising at least 132 amino acids of the C-terminus of a MTB32A antigen (SEQ ID NO:2 or 4).
 58. The method of claim 56, wherein the nucleic acid encodes a fusion polypeptide having the amino acid sequence of MTB59F (SEQ ID NO:20).
 59. The method of claim 58, wherein the nucleic acid has the nucleotide sequence of the nucleic acid encoding MTB59F (SEQ IDNO: 19).
 60. The method of claim 57, wherein the nucleic acid encodes a fusion polypeptide having the amino acid sequence of MTB72F (SEQ ID NO:16).
 61. The method of claim 57, wherein the nucleic acid encodes a fusion polypeptide having the amino acid sequence of MTB72FMutSA (SEQ ID NO:18).
 62. The method of claim 60, wherein the nucleic acid has the nucleotide sequence of the nucleic acid encoding MTB72F (SEQ ID NO:15).
 63. The method of claim 60, wherein the nucleic acid has the nucleotide sequence of the nucleic acid encoding MTB72FMutSA (SEQ ID NO:17).
 64. An isolated nucleic acid encoding a MTB32A antigen from a Mycobacterium species of the tuberculosis complex, wherein at least one amino acid in the active site triad of the MTB32A antigen (SEQ ID NO:2 or 4) has been substituted by a different amino acid.
 65. The nucleic acid of claim 64, wherein an serine residue corresponding to amino acid position 183 of SEQ ID NO:4 or position 207 of SEQ ID NO:2 has been substituted by another amino acid.
 66. The nucleic acid of claim 65, wherein an alanine residue has been substituted for the serine residue.
 67. The nucleic acid of claim 66, wherein the nucleic acid comprises a nucleotide sequence of SEQ ID NO:5.
 68. A composition comprising the nucleic acid of claim
 64. 69. A nucleic acid encoding a fusion polypeptide comprising the nucleic acid of claim
 64. 70. An isolated MTB32A polypeptide from a Mycobacterium species of the tuberculosis complex, wherein at least one amino acid in the active site triad of the MTB32A antigen (SEQ ID NO:2 or 4) has been substituted by a different amino acid.
 71. The polypeptide of claim 70, wherein a serine residue corresponding to amino acid position 183 of SEQ ID NO:4 or amino acid position 207 of SEQ ID NO:2 has been substituted by another amino acid.
 72. The polypeptide of claim 71, wherein an alanine residue has been substituted for the serine residue.
 73. A polypeptide of claim 72, wherein the polypeptide comprises an amino acid sequence of SEQ ID NO:6.
 74. A composition comprising the polypeptide of claim
 70. 75. A fusion polypeptide comprising the polypeptide of claim
 70. 76. An isolated nucleic acid encoding a fusion polypeptide comprising a MTB39 antigen (SEQ ID NO:12 or 14) from a Mycobacterium species of the tuberculosis complex, and an antigen comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex, wherein an amino acid of the active site triad of the MTB32A antigen (SEQ ID NO:2 or 4) has been substituted by a different amino acid.
 77. The nucleic acid of claim 76, wherein a serine residue corresponding to amino acid at position 183 of SEQ ID NO:4 or position 207 or SEQ ID NO:2 has been substituted by another amino acid.
 78. The nucleic acid of claim 77, wherein an alanine residue has been substituted for the serine residue.
 79. A composition comprising the nucleic acid of claim
 76. 80. A nucleic acid encoding a fusion polypeptide comprising the nucleic acid of claim
 76. 81. A nucleic acid encoding a fusion polypeptide, wherein the nucleic acid comprises a nucleotide sequence of SEQ ID NO:17.
 82. A nucleic acid encoding a fusion polypeptide comprising an amino acid sequence of SEQ ID NO:18.
 83. An isolated polypeptide encoding a fusion polypeptide comprising a MTB39 (SEQ ID NO: 12 or 14) antigen from a Mycobacterium species of the tuberculosis complex, and an antigen comprising at least 195 amino acids from the N-terminus of a MTB32A antigen (SEQ ID NO:2 or 4) from a Mycobacterium species of the tuberculosis complex, wherein an amino acid of the active site triad of the MTB32A antigen (SEQ ID NO:2 or 4) has been substituted by a different amino acid.
 84. The polypeptide of claim 83, wherein an serine residue corresponding to amino acid position 183 of SEQ ID NO:4 or amino acid position 207 of SEQ ID NO:2 has been substituted by another amino acid.
 85. The polypeptide of claim 83, wherein an alanine residue has been substituted for the serine residue.
 86. A composition comprising the polypeptide of claim
 83. 87. A fusion polypeptide comprising the polypeptide of claim
 83. 88. A fusion polypeptide comprising an amino acid sequence of SEQ ID NO:18. 